Contents

1 Setup script

The package OmicSelector has a lot of requirements that are nessesary to run all the experiments. The script below will allow to install most of them. It is highly recommended to install those packages using the code below.

If you are using our docker enviorment to learn this package you should not run this again. It would be a waste of time. [However, if you wish, you can play with the code in the notebook. Click here.](If you are using our enviorment to learn this package you can tweak this code in the interactive notebook. Click here.

Setup script:

readLines("https://raw.githubusercontent.com/kstawiski/OmicSelector/master/vignettes/setup.R") %>% paste0(collapse = "\n") %>% cat
#> ## Default repo
#> # Ubuntu: apt install default-jre default-jdk libmagick++-dev zlib1g-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev r-cran-rgl
#> r = getOption("repos")
#> r["CRAN"] = "https://cran.r-project.org"
#> options(repos = r)
#> 
#> 
#> tylko_cran = c("BiocManager","devtools","reticulate","remotes","keras")
#> if (length(setdiff(tylko_cran, rownames(installed.packages()))) > 0) {
#>   install.packages(setdiff(tylko_cran, rownames(installed.packages())), ask = F)  }
#> 
#> packages = c("remotes","devtools","parallel","rlang","ps","roxygen2", "plotly", "rJava", "mice","BiocManager", "MatchIt","curl",
#>                        "reticulate", "kableExtra","plyr","dplyr","edgeR","epiDisplay","rsq","MASS","Biocomb","caret","dplyr",
#>                        "pROC","ggplot2","DMwR", "doParallel", "Boruta", "spFSR", "varSelRF", "stringr", "psych", "C50", "randomForest", "doParallel",
#>                        "foreach","data.table", "ROSE", "deepnet", "gridExtra", "stargazer","gplots","My.stepwise","snow", "sva", "Biobase",
#>                        "calibrate", "ggrepel", "networkD3", "VennDiagram","RSNNS", "kernlab", "car", "PairedData",
#>                        "profileR","classInt","kernlab","xgboost", "keras", "tidyverse", "cutpointr","tibble","tidyr",
#>                        "rpart", "party", "mgcv", "GDCRNATools", "rJava", "cutpointr", "HTqPCR", "nondetects",
#>                        "imputeMissings", "visdat", "naniar", "stringr", "R.utils", "TCGAbiolinks", "GDCRNATools",
#>                        "kableExtra", "VIM", "mice", "MatchIt", "XML", "rmarkdown", "xtable", "ComplexHeatmap","circlize",
#>                        "BiocStyle","magick", "BiocCheck","cluster","tidyselect","ellipsis","funModeling", "mnormt","xlsx")
#> 
#> if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
#>   BiocManager::install(setdiff(packages, rownames(installed.packages())), ask = F)  }
#> 
#> library(devtools)
#> library(remotes)
#> # Paczki z githuba
#> if("bounceR" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("STATWORX/bounceR") }
#> if("ggbiplot" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("vqv/ggbiplot") }
#> if("mnormt" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("cran/mnormt") }
#> if("purrrogress" %in% rownames(installed.packages()) == FALSE) {  remotes::install_github("halpo/purrrogress") } 
#> 
#> 
#> # tryCatch(
#> #         {
#> #             if(grepl("64", Sys.info()[["machine"]], fixed = TRUE)) {
#> #             # Keras
#> #             library(keras)
#> #             if(!keras::is_keras_available()) {
#> 
#> #               install_keras() }
#> #             } else { message("\n\n!!!!! If you are not running 64-bit based machine you might experience problems with keras and tensorflow that are unrelated to this package. !!!!!\n\n") }
#> 
#> #         },
#> #         error=function(cond) {
#> #             message(cond)
#> #             message("Unable to verify the correctness of keras installation. Please run keras::install_keras() later.")
#> #         },
#> #         warning=function(cond) {
#> #             message(cond)
#> #             message("Unable to verify the correctness of keras installation. Please run keras::install_keras() later.")
#> #         },
#> #         finally={
#> 
#> #         }
#> #     )
#> 
#> if(grepl("64", Sys.info()[["machine"]], fixed = TRUE) && !keras::is_keras_available()) { message("Keras is not installed. Please run keras::install_keras() later.") }
#> 
#> # OmicSelector
#> if("OmicSelector" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("kstawiski/OmicSelector", upgrade = "never") }
#> message("OK! OmicSelector is installed correctly!")

This code does not cover the installation of mxnet, which can be used for benchmarking of the selected miRNA sets. The mxnet is however built and installed in our docker enviorment.

As the OmicSelector package is installed we can load it easly.

library(OmicSelector)

2 Getting the data

To present the package functionality, we will use the pan-cancer data from TCGA (https://portal.gdc.cancer.gov/repository). These two commands below will download and store all the necessary data in your working directory. Please note, that this process may take some time (depending on your network connection), but has to be performed only once.

OmicSelector_download_tissue_miRNA_data_from_TCGA()
OmicSelector_process_tissue_miRNA_TCGA(remove_miRNAs_with_null_var = T)

Both of those function produce 2 files: tissue_miRNA_counts.csv and tissue_miRNA_logtpm.csv. First of those files contains metadata and raw counts as declared in TCGA. The second is are log-transformed transcripts-per-million (TPM) counts. Let’s load counts files and see its summary.

suppressWarnings(suppressMessages(library(data.table)))
suppressWarnings(suppressMessages(library(knitr)))
data("orginal_TCGA_data")
OmicSelector_table(table(orginal_TCGA_data$primary_site, orginal_TCGA_data$sample_type))
PrimaryTumor SolidTissueNormal
Adrenal gland 80 0
Bladder 409 19
Brain 512 5
Breast 1078 104
Bronchus and lung 991 91
Cervix uteri 307 3
Corpus uteri|Stomach|Other and unspecified parts of tongue|Meninges|Other and unspecified male genital organs|Colon|Connective, subcutaneous and other soft tissues|Bones, joints and articular cartilage of limbs|Ovary|Retroperitoneum and peritoneum|Peripheral nerves and autonomic nervous system|Uterus, NOS|Kidney 259 0
Corpus uteri|Uterus, NOS 538 33
Esophagus|Stomach 184 13
Eye and adnexa 80 0
Heart, mediastinum, and pleura|Bronchus and lung 87 0
Heart, mediastinum, and pleura|Other endocrine glands and related structures|Adrenal gland|Connective, subcutaneous and other soft tissues|Other and ill-defined sites|Spinal cord, cranial nerves, and other parts of central nervous system|Retroperitoneum and peritoneum 179 3
Heart, mediastinum, and pleura|Testis|Stomach|Lymph nodes|Bones, joints and articular cartilage of other and unspecified sites|Brain|Thyroid gland|Small intestine|Colon|Connective, subcutaneous and other soft tissues|Other and unspecified major salivary glands|Retroperitoneum and peritoneum|Hematopoietic and reticuloendothelial systems|Breast 47 0
Heart, mediastinum, and pleura|Thymus 124 2
Kidney 873 130
Liver and intrahepatic bile ducts 372 50
Other and ill-defined sites in lip, oral cavity and pharynx|Palate|Other and unspecified parts of tongue|Hypopharynx|Tonsil|Oropharynx|Larynx|Other and unspecified parts of mouth|Gum|Floor of mouth|Bones, joints and articular cartilage of other and unspecified sites|Lip|Base of tongue 523 44
Other and unspecified parts of biliary tract|Gallbladder|Liver and intrahepatic bile ducts 36 9
Ovary 489 0
Pancreas 178 4
Prostate gland 494 52
Rectosigmoid junction|Colon 444 8
Rectosigmoid junction|Unknown|Rectum|Colon|Connective, subcutaneous and other soft tissues 161 3
Skin 97 2
Stomach 436 41
Testis 150 0
Thyroid gland 506 59
Uterus, NOS 57 0

Let’s consider a following exemplary problem..

We want to find the set of miRNAs the most specific to pancreatic cancer. We see that there are 178 cases of pancreatic cancer miRNA-seq results and only 4 solid tissue normal cases. However, we have multiple normal tissue miRNA-seq results from other projects that could be incorporated in the analysis. Let’s filter and label the samples of interest.

suppressWarnings(suppressMessages(library(dplyr)))

cancer_cases = filter(orginal_TCGA_data, primary_site == "Pancreas" & sample_type == "PrimaryTumor")
control_cases = filter(orginal_TCGA_data, sample_type == "SolidTissueNormal")

The pipeline requires the variable Class with two levels (Cancer and Control) to be present in the dataset.

cancer_cases$Class = "Cancer"
control_cases$Class = "Control"

dataset = rbind(cancer_cases, control_cases)

OmicSelector_table(table(dataset$Class), col.names = c("Class", "Number of cases"))
Class Number of cases
Cancer 178
Control 675 
boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 3.88, df = 360.55, p-value = 0.0001242
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>   693.0905 2117.7294
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              22376.82
OmicSelector_table(table(dataset$gender.x, dataset$Class))
Cancer Control
female 80 334
male 98 325 
chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 1.6241, df = 1, p-value = 0.2025

There is a stistically significant difference in age between classess. The gender was not associated with class. In order to increase feature selection performance, we will try to balance the sets by performing propensity score matching.

old_dataset = dataset  # backup
dataset = dataset[grepl("Adenocarcinomas", dataset$disease_type), ]
match_by = c("age_at_diagnosis", "gender.x")
tempdane = dplyr::select(dataset, match_by)
tempdane$Class = ifelse(dataset$Class == "Cancer", TRUE, FALSE)
suppressMessages(library(mice))
suppressMessages(library(MatchIt))
temp1 = mice(tempdane, m = 1)
#> 
#>  iter imp variable
#>   1   1  age_at_diagnosis
#>   2   1  age_at_diagnosis
#>   3   1  age_at_diagnosis
#>   4   1  age_at_diagnosis
#>   5   1  age_at_diagnosis
temp2 = temp1$data
temp3 = mice::complete(temp1)
temp3 = temp3[complete.cases(temp3), ]
tempform = OmicSelector_create_formula(match_by)
mod_match <- matchit(tempform, data = temp3)
newdata = match.data(mod_match)
dataset = dataset[as.numeric(rownames(newdata)), ]

Let’s check if there is any imbalance in the new, transformed dataset.

boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 0.090876, df = 351.63, p-value = 0.9276
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  -827.5374  907.7172
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              23742.14
OmicSelector_table(table(dataset$gender.x, dataset$Class))
Cancer Control
female 80 79
male 98 99 
chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 0, df = 1, p-value = 1
fwrite(dataset, "balanced_dataset.csv.gz")
OmicSelector_tutorial_balanced_dataset = dataset  # can be used by data('OmicSelector_tutorial_balanced_dataset')

There are no significant differences in age or gender composition between classes now. We can proceed to standard filtering, log-transormation and TPM-normalization.

However, first, in order to stay consistent between different datasets, we need to standardise microRNA names. OmicSelector_correct_miRNA_names() unify the miRNA names between different versions of miRbase.

dataset = OmicSelector_correct_miRNA_names(dataset)  # Correct miRNA names based on the aliases. Useful when analyzing old datasets - to keep the results coherent with current knowledge.
danex = dplyr::select(dataset, starts_with("hsa"))  # Create data.frame or matrix with miRNA counts with miRNAs in columns and cases in rows.
metadane = dplyr::select(dataset, -starts_with("hsa"))  # Metadata with 'Class' variables.
OmicSelector_table(table(metadane$Class))  # Let's be sure that 'Class' variable is correct and contains only 'Cancer' and 'Control' cases.
Var1 Freq
Cancer 178
Control 178 
ttpm = OmicSelector_counts_to_log10tpm(danex, metadane, ids = metadane$sample, filtr = T, filtr_minimalcounts = 100, filtr_howmany = 1/3)  # We will leave only the miRNAs which apeared with at least 100 counts in 1/3 of cases.
#> 
#> DGEList unfiltered object with TPM was saved as TPM_DGEList.rds.
#> DGEList filtered object with TPM was saved as TPM_DGEList_filtered.rds.
#> (After filtering) miRNAs left: 166 | filtered out: 2418.
#> Returned data are log10(TPM).

You might have noticed, that we have filtered out microRNAs not having at least 100 counts in 1/3 of samples. It was done to ensure that microRNAs selected as features for classifier (possibly used in clinic) would be detectable in other, cheaper methods, such as qPCR. After filtering there are 166 miRNAs left.

In the next step we will devide the dataset into training, testing and validation datasets. We strongly belive that hold-out validation is the most redundant validation method and although OmicSelector supports cross-validation, the hold-out validation is set by default in most cases. Thus, the rest of the analysis is dependent on existance of 3 seperate datasets:

The best signiture (best set of miRNAs for diagnostic test) can be selected based on all 3 datasets, 2 datasets or only validation set. The process of best signiture selection will be discussed below.

The split can be prepared manually by user (the pipeline expects to find mixed_*.csv files in working directory) or in a convinient way using OmicSelector_prepare_split(). Let’s do it now.

mixed = OmicSelector_prepare_split(metadane = metadane, ttpm = ttpm, train_proc = 0.6)
#> 
#> Saved 3 sets as csv in working directory. Retruned mixed dataset.
OmicSelector_tutorial_balanced_mixed = mixed  # can be used by data('OmicSelector_tutorial_balanced_mixed')

Let’s see a split summary.

mixed = fread("mixed.csv")
OmicSelector_table(table(mixed$Class, mixed$mix))
test train valid
Cancer 36 107 35
Control 36 107 35 
OmicSelector_table(cbind(mixed[1:10, c(100:105)], Class = mixed[1:10, "Class"]))
hsa-miR-30c-5p hsa-miR-30c-2-3p hsa-miR-30d-5p hsa-miR-139-5p hsa-miR-10a-5p hsa-miR-10b-5p Class.Class
2.598949 1.514444 3.802908 1.555401 4.735516 4.298381 Cancer
2.391663 1.416540 3.656058 1.326116 4.615369 3.946954 Cancer
2.576255 1.566166 3.721311 1.220338 4.385001 3.998914 Cancer
2.260492 1.401010 3.539243 1.924365 3.945605 4.486228 Cancer
2.595315 1.562735 3.571441 1.721510 4.519249 4.126032 Cancer
2.632860 1.723000 3.708020 2.120359 4.875796 3.887056 Cancer
2.747742 2.016887 3.852090 1.533525 3.961177 3.642831 Cancer
3.037578 1.880192 3.960987 1.798007 4.675070 4.133894 Cancer
2.598933 1.291485 3.581714 1.413095 4.580566 3.960672 Cancer
2.829601 1.494520 3.589292 1.755581 4.687104 4.209582 Cancer

We can see that the dataset was devided in balanced way. Now we are ready to move to the analysis…

3 Basic exploratory analysis

In biomarker studies we relay on validation. We perform hold-out validation, so the signature selection has to be based on training dataset only. Including testing and validation dataset in the exploratory analysis could lead to bias (‘data leakage’). In the following section we show how to use our package to perform quick exploratory analysis of miRNA-seq data.

dane = OmicSelector_load_datamix(use_smote_not_rose = T)  # load mixed_*.csv files
train = dane[[1]]
test = dane[[2]]
valid = dane[[3]]
train_smoted = dane[[4]]
trainx = dane[[5]]
trainx_smoted = dane[[6]]  # get the objects from list to make the code more readable.

ks_load_datamix() function loads the data created in preparation phase. It requires the output constructed by OmicSelector_prepare_split() function to be placed in working directory (‘wd’), thus files ‘mixed_train.csv’, ‘mixed_test.csv’ and ‘mixed_valid.csv’ have to exist in the directory. If you have split the data manually, there may be some imbalance of classes in train, test or validation datasets. If so, OmicSelector_prepare_split() perform balancing using:

  1. ROSE (default): https://journal.r-project.org/archive/2014/RJ-2014-008/RJ-2014-008.pdf - by default we generate 10 * number of cases in orginal dataset.
  2. SMOTE: https://arxiv.org/abs/1106.1813 - by defult we use ‘perc.under=100’ and ‘k=10’.

At the beging of the analysis we usually perform principal component analysis (PCA) to assess for any batch effect, possible outliers and get a general understanding of miRNA profile. The package can construct 2-dimentional biplot and 3-dimentional interactive scatterplot based on the computed components.

pca = OmicSelector_PCA(trainx, train$Class)
pca

3D PCA plot may not be shown correctly in Jupyter notebook, but you can check in e.g. R Studio that it worOmicSelector_

if (is.null(sessionInfo()$loadedOnly$IRdisplay)) {
    # if not in the Jupyter, if you run OmicSelector_PCA_3D in learning/editing Jupyter enviorment it may cause: *** caught segfault *** address 0x1, cause 'memory
    # not mapped'
    pca3d = OmicSelector_PCA_3D(trainx, train$Class)
    pca3d
}

Now we can also correct the batch effect, if there is any. For example, you can use OmicSelector_combat() to do so. However, detailed demonstration is out of scope of this tutorial.

Usually, the next step in the exploratory analysis is to perform the differential expression analysis. Differential expression in our package is biomarker-discovery oriented, thus it uses t-test with the correction for multiple comparisons. The following table shows signifiantly differently expressed miRNAs after Benjamini-Hochberg correction.

de = OmicSelector_differential_expression_ttest(trainx, train$Class)
sig_de = de %>% dplyr::filter(`p-value BH` <= 0.05) %>% dplyr::arrange(`p-value BH`)  # leave only significant after Benjamini-Hochberg procedure and sort by ascending p-value
OmicSelector_table(sig_de)
miR mean logtpm median logtpm SD logtpm cancer mean cancer median cancer SD control mean control median control SD log10FC (subtr estim) log10FC log2FC reversed_log10FC reversed_log2FC p-value p-value Bonferroni p-value Holm p-value BH
hsa.miR.21.5p 5.081371 5.120977 0.5409456 5.473043 5.559281 0.3042087 4.689698 4.744446 0.4309906 0.7833450 0.7833450 2.6022157 -0.7833450 -2.6022157 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30e.3p 3.654915 3.620465 0.2922656 3.445100 3.469065 0.1835853 3.864731 3.891680 0.2215066 -0.4196304 -0.4196304 -1.3939819 0.4196304 1.3939819 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30a.3p 3.861758 3.760500 0.5107622 3.494206 3.528067 0.2957390 4.229311 4.315264 0.4049904 -0.7351047 -0.7351047 -2.4419651 0.7351047 2.4419651 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30c.2.3p 1.791478 1.685323 0.4609305 1.478041 1.473434 0.2548946 2.104915 2.062559 0.4044845 -0.6268741 -0.6268741 -2.0824306 0.6268741 2.0824306 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.132.3p 2.062941 2.061854 0.3206914 2.268277 2.222890 0.2453178 1.857606 1.842071 0.2476985 0.4106709 0.4106709 1.3642193 -0.4106709 -1.3642193 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.375.3p 3.851381 4.088129 1.1312626 4.572062 4.593208 0.6167635 3.130699 3.420583 1.0689350 1.4413633 1.4413633 4.7881053 -1.4413633 -4.7881053 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.217.5p 2.065790 1.932856 1.2184284 2.817892 2.596188 1.0079357 1.313689 1.247738 0.9084168 1.5042026 1.5042026 4.9968529 -1.5042026 -4.9968529 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.139.5p 1.916157 1.919751 0.4638487 1.634747 1.558070 0.3573670 2.197567 2.204857 0.3804627 -0.5628209 -0.5628209 -1.8696506 0.5628209 1.8696506 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.199a.5p 3.034892 3.117770 0.3929526 3.267832 3.318017 0.2924584 2.801951 2.808411 0.3394148 0.4658802 0.4658802 1.5476204 -0.4658802 -1.5476204 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.338.3p 2.743796 2.778247 0.4190933 2.991348 2.994550 0.3219668 2.496243 2.539407 0.3543332 0.4951049 0.4951049 1.6447027 -0.4951049 -1.6447027 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.199b.5p 2.146095 2.358829 0.6145137 2.504540 2.573683 0.3567535 1.787650 1.799962 0.6100440 0.7168901 0.7168901 2.3814574 -0.7168901 -2.3814574 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.127.5p 2.214220 2.327709 0.4803146 2.486170 2.478848 0.3020641 1.942270 1.939357 0.4722596 0.5438996 0.5438996 1.8067954 -0.5438996 -1.8067954 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.381.3p 1.720930 1.791253 0.4579339 1.974984 1.949285 0.3353016 1.466877 1.476716 0.4226746 0.5081072 0.5081072 1.6878957 -0.5081072 -1.6878957 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.127.3p 2.789656 2.829601 0.3874414 2.995898 3.006282 0.3147991 2.583413 2.568116 0.3415622 0.4124850 0.4124850 1.3702456 -0.4124850 -1.3702456 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.199a.3p 3.431280 3.533249 0.3595668 3.620030 3.670480 0.2685999 3.242530 3.285480 0.3401837 0.3775004 0.3775004 1.2540293 -0.3775004 -1.2540293 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.181b.5p 2.447025 2.523360 0.4131408 2.664941 2.705753 0.2848923 2.229109 2.205351 0.4073655 0.4358316 0.4358316 1.4478013 -0.4358316 -1.4478013 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.199b.3p 3.430095 3.531945 0.3598114 3.619075 3.669630 0.2686093 3.241115 3.284615 0.3404382 0.3779599 0.3779599 1.2555557 -0.3779599 -1.2555557 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.194.5p 3.119571 3.359054 0.8329947 3.562675 3.633752 0.4167141 2.676468 2.410622 0.9078933 0.8862067 0.8862067 2.9439150 -0.8862067 -2.9439150 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.134.5p 2.366486 2.433393 0.4088244 2.572458 2.557931 0.2993653 2.160514 2.115254 0.4007277 0.4119434 0.4119434 1.3684465 -0.4119434 -1.3684465 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30a.5p 4.429837 4.356060 0.4519742 4.199892 4.226049 0.2683567 4.659782 4.685628 0.4813796 -0.4598896 -0.4598896 -1.5277200 0.4598896 1.5277200 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.200a.5p 2.480123 2.527551 0.5262405 2.744628 2.777438 0.3622178 2.215619 2.330898 0.5329388 0.5290086 0.5290086 1.7573286 -0.5290086 -1.7573286 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.136.5p 1.426048 1.539528 0.5852494 1.722033 1.713813 0.2950712 1.130063 1.259715 0.6514071 0.5919692 0.5919692 1.9664791 -0.5919692 -1.9664791 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.192.5p 3.474000 3.723466 0.8856187 3.920081 3.942126 0.4108526 3.027920 2.831424 1.0027511 0.8921615 0.8921615 2.9636965 -0.8921615 -2.9636965 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.451a 2.540774 2.525599 0.6339915 2.233131 2.192706 0.4710976 2.848417 2.906464 0.6282318 -0.6152860 -0.6152860 -2.0439357 0.6152860 2.0439357 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.200a.3p 2.330223 2.419049 0.6863313 2.660594 2.674894 0.3970887 1.999851 2.171325 0.7539997 0.6607432 0.6607432 2.1949415 -0.6607432 -2.1949415 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.141.3p 2.470222 2.587047 0.6758787 2.787653 2.835787 0.4142754 2.152790 2.366831 0.7368061 0.6348621 0.6348621 2.1089664 -0.6348621 -2.1089664 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.181c.3p 1.549848 1.598609 0.3058360 1.691125 1.690791 0.2009568 1.408572 1.397065 0.3275293 0.2825529 0.2825529 0.9386203 -0.2825529 -0.9386203 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30d.5p 3.824938 3.786939 0.2585958 3.705810 3.708020 0.1763818 3.944065 3.950384 0.2731545 -0.2382549 -0.2382549 -0.7914657 0.2382549 0.7914657 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.200b.3p 2.716967 2.769036 0.5121158 2.949316 3.014389 0.3627291 2.484618 2.625241 0.5351976 0.4646977 0.4646977 1.5436922 -0.4646977 -1.5436922 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.708.3p 1.553047 1.799718 0.7046857 1.878493 1.937453 0.3169286 1.227601 1.186108 0.8267867 0.6508920 0.6508920 2.1622164 -0.6508920 -2.1622164 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.210.3p 2.239766 2.271507 0.6889295 2.547543 2.542301 0.5385826 1.931988 2.106523 0.6873228 0.6155552 0.6155552 2.0448301 -0.6155552 -2.0448301 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.486.5p 2.102968 2.062283 0.6191482 1.830616 1.754483 0.4121882 2.375321 2.342782 0.6713086 -0.5447046 -0.5447046 -1.8094696 0.5447046 1.8094696 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.29a.3p 3.841416 3.818064 0.2415932 3.736185 3.745283 0.1796643 3.946646 3.954986 0.2503002 -0.2104605 -0.2104605 -0.6991346 0.2104605 0.6991346 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.378a.3p 2.550650 2.512377 0.3937521 2.378397 2.381114 0.2557418 2.722903 2.778885 0.4315532 -0.3445063 -0.3445063 -1.1444252 0.3445063 1.1444252 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.379.5p 2.828974 2.918613 0.4091041 3.006836 3.034753 0.2966347 2.651112 2.644205 0.4294792 0.3557240 0.3557240 1.1816895 -0.3557240 -1.1816895 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.141.5p 2.216028 2.392275 0.6525748 2.500775 2.556782 0.3976527 1.931282 2.148570 0.7306892 0.5694928 0.5694928 1.8918140 -0.5694928 -1.8918140 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.21.3p 2.950511 3.002843 0.4495447 3.143884 3.238660 0.3956108 2.757137 2.698429 0.4172376 0.3867473 0.3867473 1.2847466 -0.3867473 -1.2847466 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.337.3p 1.498952 1.609902 0.4286748 1.685506 1.704399 0.2599192 1.312398 1.278140 0.4810808 0.3731072 0.3731072 1.2394354 -0.3731072 -1.2394354 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.144.5p 1.799486 1.840358 0.7365132 1.481479 1.461856 0.4729441 2.117492 2.202314 0.8137450 -0.6360122 -0.6360122 -2.1127868 0.6360122 2.1127868 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.429 1.847904 1.950131 0.7268633 2.162646 2.205144 0.3857231 1.533162 1.702486 0.8443154 0.6294838 0.6294838 2.0910999 -0.6294838 -2.0910999 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.335.3p 1.773607 1.812886 0.3718545 1.932716 1.892784 0.2426583 1.614497 1.631930 0.4097115 0.3182195 0.3182195 1.0571023 -0.3182195 -1.0571023 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.126.5p 2.232491 2.222927 0.4152358 2.056938 2.063790 0.2104761 2.408045 2.529680 0.4898455 -0.3511067 -0.3511067 -1.1663511 0.3511067 1.1663511 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.30c.5p 2.808698 2.749100 0.3490929 2.661967 2.661797 0.1963921 2.955429 2.915562 0.4035411 -0.2934616 -0.2934616 -0.9748585 0.2934616 0.9748585 0.0000000 0.0000000 0.0000000 0.0000000
hsa.miR.181a.3p 2.106380 2.174268 0.3784895 2.261578 2.305816 0.2347854 1.951183 2.028792 0.4290792 0.3103947 0.3103947 1.0311087 -0.3103947 -1.0311087 0.0000000 0.0000001 0.0000001 0.0000000
hsa.let.7c.5p 3.419322 3.422382 0.3296842 3.287237 3.332260 0.2860501 3.551407 3.535984 0.3183740 -0.2641699 -0.2641699 -0.8775535 0.2641699 0.8775535 0.0000000 0.0000002 0.0000001 0.0000000
hsa.miR.181a.5p 3.155295 3.246986 0.4050583 3.316282 3.343112 0.2324404 2.994307 2.991241 0.4725895 0.3219750 0.3219750 1.0695778 -0.3219750 -1.0695778 0.0000000 0.0000004 0.0000003 0.0000000
hsa.miR.221.3p 2.290528 2.336670 0.3527519 2.427381 2.408816 0.2861108 2.153674 2.182603 0.3610694 0.2737072 0.2737072 0.9092357 -0.2737072 -0.9092357 0.0000000 0.0000007 0.0000005 0.0000000
hsa.miR.93.5p 3.298589 3.328666 0.2589551 3.398683 3.400925 0.1891085 3.198495 3.236571 0.2806412 0.2001879 0.2001879 0.6650098 -0.2001879 -0.6650098 0.0000000 0.0000009 0.0000006 0.0000000
hsa.miR.378a.5p 1.765728 1.699123 0.3998851 1.610886 1.612851 0.2430057 1.920570 1.955764 0.4624594 -0.3096836 -0.3096836 -1.0287466 0.3096836 1.0287466 0.0000000 0.0000011 0.0000008 0.0000000
hsa.miR.146b.5p 2.601785 2.674141 0.4626849 2.779955 2.835954 0.2919913 2.423615 2.450139 0.5299317 0.3563393 0.3563393 1.1837335 -0.3563393 -1.1837335 0.0000000 0.0000013 0.0000009 0.0000000
hsa.miR.23a.3p 3.411765 3.464466 0.2170216 3.494149 3.504609 0.1702973 3.329380 3.342163 0.2278979 0.1647689 0.1647689 0.5473504 -0.1647689 -0.5473504 0.0000000 0.0000016 0.0000011 0.0000000
hsa.miR.30b.5p 2.622413 2.622930 0.3212403 2.499914 2.507222 0.2120817 2.744913 2.792110 0.3634422 -0.2449988 -0.2449988 -0.8138683 0.2449988 0.8138683 0.0000000 0.0000017 0.0000012 0.0000000
hsa.miR.625.3p 2.068354 2.104397 0.3502308 2.200772 2.210917 0.2188272 1.935936 1.910435 0.4039743 0.2648357 0.2648357 0.8797652 -0.2648357 -0.8797652 0.0000000 0.0000025 0.0000017 0.0000000
hsa.miR.182.5p 3.674023 3.755735 0.4922991 3.858145 3.842168 0.3744427 3.489902 3.616382 0.5275933 0.3682429 0.3682429 1.2232765 -0.3682429 -1.2232765 0.0000000 0.0000029 0.0000020 0.0000001
hsa.miR.27a.3p 3.005903 3.044024 0.2647920 3.104509 3.109418 0.2287859 2.907296 2.903005 0.2625226 0.1972135 0.1972135 0.6551290 -0.1972135 -0.6551290 0.0000000 0.0000030 0.0000020 0.0000001
hsa.miR.183.5p 3.203446 3.257163 0.4833569 3.381328 3.357706 0.3966813 3.025563 3.143805 0.4982314 0.3557648 0.3557648 1.1818251 -0.3557648 -1.1818251 0.0000000 0.0000047 0.0000031 0.0000001
hsa.miR.181c.5p 1.665600 1.682222 0.3601516 1.795267 1.778815 0.2462991 1.535932 1.501756 0.4074728 0.2593354 0.2593354 0.8614935 -0.2593354 -0.8614935 0.0000001 0.0000115 0.0000076 0.0000002
hsa.miR.126.3p 3.305734 3.272928 0.4223713 3.157448 3.162873 0.2190488 3.454020 3.630912 0.5158520 -0.2965719 -0.2965719 -0.9851906 0.2965719 0.9851906 0.0000002 0.0000319 0.0000209 0.0000005
hsa.miR.582.3p 2.087755 2.119436 0.3376004 1.973266 1.974597 0.2964765 2.202245 2.291615 0.3386179 -0.2289783 -0.2289783 -0.7606496 0.2289783 0.7606496 0.0000004 0.0000584 0.0000380 0.0000010
hsa.miR.143.3p 4.940749 4.860769 0.4133211 4.799815 4.796805 0.2682101 5.081683 4.987285 0.4808783 -0.2818686 -0.2818686 -0.9363472 0.2818686 0.9363472 0.0000004 0.0000618 0.0000398 0.0000010
hsa.miR.185.5p 1.698820 1.752167 0.3122312 1.803017 1.789962 0.1825995 1.594623 1.585711 0.3750133 0.2083937 0.2083937 0.6922687 -0.2083937 -0.6922687 0.0000007 0.0001204 0.0000769 0.0000020
hsa.miR.29c.3p 3.321214 3.327217 0.3591607 3.202955 3.215627 0.2277490 3.439473 3.491354 0.4232090 -0.2365180 -0.2365180 -0.7856959 0.2365180 0.7856959 0.0000010 0.0001621 0.0001026 0.0000026
hsa.miR.223.3p 2.257390 2.288581 0.4632869 2.408097 2.462940 0.4003810 2.106684 2.111760 0.4744849 0.3014129 0.3014129 1.0012719 -0.3014129 -1.0012719 0.0000011 0.0001834 0.0001149 0.0000029
hsa.miR.423.5p 1.545436 1.538957 0.3144486 1.443133 1.425446 0.2069216 1.647738 1.666376 0.3670736 -0.2046048 -0.2046048 -0.6796823 0.2046048 0.6796823 0.0000013 0.0002154 0.0001337 0.0000034
hsa.miR.151a.5p 1.778564 1.824896 0.2355297 1.854691 1.836098 0.1493639 1.702436 1.739749 0.2783202 0.1522549 0.1522549 0.5057800 -0.1522549 -0.5057800 0.0000016 0.0002604 0.0001600 0.0000040
hsa.let.7i.5p 2.599921 2.632392 0.2997045 2.696086 2.717300 0.1738861 2.503755 2.466912 0.3627486 0.1923305 0.1923305 0.6389080 -0.1923305 -0.6389080 0.0000020 0.0003296 0.0002005 0.0000050
hsa.miR.26b.5p 2.777405 2.755033 0.2942712 2.683523 2.667076 0.2076405 2.871288 2.871957 0.3363026 -0.1877642 -0.1877642 -0.6237392 0.1877642 0.6237392 0.0000020 0.0003363 0.0002026 0.0000050
hsa.miR.222.3p 1.679643 1.690400 0.3421027 1.788188 1.797616 0.2933599 1.571098 1.634996 0.3540146 0.2170897 0.2170897 0.7211563 -0.2170897 -0.7211563 0.0000021 0.0003468 0.0002068 0.0000051
hsa.miR.320a.3p 2.517259 2.510587 0.2335402 2.443505 2.440882 0.2043264 2.591012 2.575436 0.2384649 -0.1475073 -0.1475073 -0.4900086 0.1475073 0.4900086 0.0000023 0.0003863 0.0002281 0.0000056
hsa.miR.30e.5p 3.679150 3.640665 0.3123538 3.579560 3.581958 0.1513627 3.778740 3.843580 0.3913006 -0.1991799 -0.1991799 -0.6616613 0.1991799 0.6616613 0.0000025 0.0004221 0.0002467 0.0000060
hsa.miR.200c.3p 3.479500 3.647500 0.6328315 3.679499 3.713871 0.3714689 3.279502 3.524250 0.7654977 0.3999973 0.3999973 1.3287624 -0.3999973 -1.3287624 0.0000028 0.0004717 0.0002728 0.0000066
hsa.miR.145.5p 3.405874 3.362197 0.3557557 3.294171 3.279622 0.2492612 3.517576 3.469948 0.4086525 -0.2234046 -0.2234046 -0.7421341 0.2234046 0.7421341 0.0000030 0.0004969 0.0002844 0.0000069
hsa.miR.92b.3p 1.748375 1.731752 0.3770581 1.865526 1.808052 0.2617419 1.631225 1.619889 0.4352821 0.2343014 0.2343014 0.7783325 -0.2343014 -0.7783325 0.0000039 0.0006400 0.0003624 0.0000088
hsa.miR.629.5p 1.718671 1.767577 0.2822432 1.804344 1.819456 0.2016194 1.632997 1.650836 0.3234272 0.1713470 0.1713470 0.5692024 -0.1713470 -0.5692024 0.0000064 0.0010697 0.0005993 0.0000145
hsa.miR.99a.5p 2.916024 2.912899 0.3862114 2.800660 2.801168 0.3181101 3.031388 3.020665 0.4143220 -0.2307282 -0.2307282 -0.7664624 0.2307282 0.7664624 0.0000086 0.0014262 0.0007904 0.0000190
hsa.miR.22.3p 4.901288 4.935034 0.2599745 4.979132 4.983023 0.1344526 4.823443 4.825832 0.3248074 0.1556883 0.1556883 0.5171853 -0.1556883 -0.5171853 0.0000101 0.0016706 0.0009158 0.0000220
hsa.miR.10b.5p 4.284825 4.160990 0.6577961 4.092498 4.126032 0.2208435 4.477153 4.339191 0.8637267 -0.3846552 -0.3846552 -1.2777969 0.3846552 1.2777969 0.0000184 0.0030501 0.0016537 0.0000396
hsa.miR.142.3p 2.908082 2.993345 0.5523317 3.062898 3.069081 0.3324835 2.753266 2.754739 0.6738583 0.3096321 0.3096321 1.0285755 -0.3096321 -1.0285755 0.0000350 0.0058148 0.0031176 0.0000745
hsa.miR.16.5p 2.418426 2.396977 0.2678058 2.344887 2.354009 0.1520643 2.491965 2.532161 0.3317754 -0.1470782 -0.1470782 -0.4885833 0.1470782 0.4885833 0.0000518 0.0086050 0.0045617 0.0001089
hsa.miR.10a.5p 4.453193 4.572159 0.4172756 4.567356 4.619375 0.2726925 4.339031 4.448143 0.4992066 0.2283251 0.2283251 0.7584795 -0.2283251 -0.7584795 0.0000528 0.0087721 0.0045974 0.0001097
hsa.miR.365a.3p 1.558982 1.524607 0.3288053 1.472455 1.482687 0.2603646 1.645509 1.646930 0.3665257 -0.1730535 -0.1730535 -0.5748714 0.1730535 0.5748714 0.0000972 0.0161318 0.0083574 0.0001970
hsa.miR.365b.3p 1.559072 1.524607 0.3286232 1.472600 1.482687 0.2598729 1.645545 1.646930 0.3665720 -0.1729456 -0.1729456 -0.5745130 0.1729456 0.5745130 0.0000973 0.0161562 0.0083574 0.0001970
hsa.miR.20a.5p 2.167170 2.188072 0.3531756 2.258504 2.252491 0.2151305 2.075836 2.092815 0.4330362 0.1826683 0.1826683 0.6068109 -0.1826683 -0.6068109 0.0001387 0.0230266 0.0116520 0.0002774
hsa.miR.195.5p 1.610326 1.644712 0.4593292 1.492892 1.530241 0.2351047 1.727760 1.829698 0.5838159 -0.2348685 -0.2348685 -0.7802161 0.2348685 0.7802161 0.0001727 0.0286635 0.0143318 0.0003412
hsa.miR.26a.5p 3.363368 3.336961 0.2249507 3.307628 3.297116 0.1471895 3.419108 3.407502 0.2715615 -0.1114806 -0.1114806 -0.3703306 0.1114806 0.3703306 0.0002606 0.0432635 0.0213711 0.0005090
hsa.miR.145.3p 1.779374 1.754841 0.2975307 1.706504 1.693139 0.2239980 1.852244 1.840403 0.3420364 -0.1457395 -0.1457395 -0.4841363 0.1457395 0.4841363 0.0002988 0.0495960 0.0242005 0.0005767
hsa.miR.142.5p 1.517108 1.642632 0.7709832 1.707036 1.728336 0.3336782 1.327180 1.413437 1.0051222 0.3798562 0.3798562 1.2618548 -0.3798562 -1.2618548 0.0003066 0.0509030 0.0245316 0.0005851
hsa.miR.155.5p 2.133480 2.195366 0.4195203 2.233687 2.297068 0.3475670 2.033272 2.006969 0.4610634 0.2004154 0.2004154 0.6657657 -0.2004154 -0.6657657 0.0004167 0.0691679 0.0329172 0.0007860
hsa.let.7d.5p 2.204108 2.185887 0.2122742 2.154807 2.147458 0.1420691 2.253409 2.269843 0.2558420 -0.0986016 -0.0986016 -0.3275473 0.0986016 0.3275473 0.0006292 0.1044446 0.0490764 0.0011735
hsa.miR.101.3p 4.064812 4.041831 0.3932389 3.975163 3.934040 0.1680979 4.154461 4.258030 0.5159943 -0.1792983 -0.1792983 -0.5956161 0.1792983 0.5956161 0.0008471 0.1406149 0.0652250 0.0015624
hsa.miR.15a.5p 1.962872 1.985385 0.2869339 2.027709 2.007988 0.1768348 1.898034 1.940992 0.3545154 0.1296752 0.1296752 0.4307717 -0.1296752 -0.4307717 0.0008984 0.1491266 0.0678151 0.0016209
hsa.miR.140.3p 3.000561 3.018035 0.2271711 2.949429 2.935298 0.2005767 3.051693 3.090265 0.2412282 -0.1022638 -0.1022638 -0.3397129 0.1022638 0.3397129 0.0008923 0.1481224 0.0678151 0.0016209
hsa.miR.193a.5p 2.336431 2.300347 0.3276854 2.266929 2.278125 0.1938504 2.405932 2.378371 0.4104126 -0.1390021 -0.1390021 -0.4617551 0.1390021 0.4617551 0.0018588 0.3085666 0.1375538 0.0033179
hsa.let.7b.5p 4.195831 4.209035 0.2924159 4.256938 4.282751 0.1889508 4.134724 4.104211 0.3585804 0.1222138 0.1222138 0.4059855 -0.1222138 -0.4059855 0.0021512 0.3570954 0.1570359 0.0037989
hsa.miR.425.5p 1.923042 1.930834 0.3243793 1.987356 1.978949 0.2395357 1.858729 1.880977 0.3817182 0.1286263 0.1286263 0.4272874 -0.1286263 -0.4272874 0.0035774 0.5938450 0.2575713 0.0062510
hsa.miR.99b.5p 4.315202 4.300285 0.2601134 4.263737 4.282048 0.1951765 4.366667 4.343604 0.3041630 -0.1029303 -0.1029303 -0.3419271 0.1029303 0.3419271 0.0036421 0.6045962 0.2585923 0.0062979
hsa.miR.146b.3p 1.886946 1.965307 0.4754291 1.979342 1.993235 0.3044790 1.794549 1.860622 0.5867326 0.1847929 0.1847929 0.6138687 -0.1847929 -0.6138687 0.0043674 0.7249845 0.3057163 0.0074741
hsa.miR.128.3p 1.955925 1.943604 0.2304255 2.000480 1.993252 0.1994596 1.911370 1.897153 0.2508004 0.0891101 0.0891101 0.2960174 -0.0891101 -0.2960174 0.0044531 0.7392212 0.3072666 0.0075431
hsa.miR.34a.5p 2.074666 2.121651 0.2675331 2.125712 2.136585 0.1931050 2.023620 2.059319 0.3182343 0.1020923 0.1020923 0.3391431 -0.1020923 -0.3391431 0.0050922 0.8453067 0.3462702 0.0085385
hsa.miR.1307.5p 2.032668 2.074195 0.4746939 2.121558 2.143052 0.3137240 1.943777 1.930948 0.5817384 0.1777808 0.1777808 0.5905749 -0.1777808 -0.5905749 0.0060341 1.0000000 0.4042856 0.0100166
hsa.miR.146a.5p 1.834930 1.878293 0.5428638 1.936147 1.968467 0.3763981 1.733712 1.804289 0.6556095 0.2024345 0.2024345 0.6724729 -0.2024345 -0.6724729 0.0062340 1.0000000 0.4114442 0.0102460
hsa.miR.660.5p 1.637156 1.706445 0.5648980 1.742335 1.736172 0.1929619 1.531977 1.656099 0.7626676 0.2103579 0.2103579 0.6987938 -0.2103579 -0.6987938 0.0065781 1.0000000 0.4275745 0.0107055
hsa.miR.1307.3p 2.668366 2.682073 0.3103661 2.725068 2.712113 0.1957961 2.611663 2.652759 0.3856627 0.1134058 0.1134058 0.3767259 -0.1134058 -0.3767259 0.0074280 1.0000000 0.4753900 0.0119713
hsa.miR.17.3p 2.280466 2.310070 0.2760079 2.330198 2.324300 0.1630184 2.230733 2.251456 0.3485844 0.0994646 0.0994646 0.3304142 -0.0994646 -0.3304142 0.0083333 1.0000000 0.5249975 0.0133012
hsa.miR.103a.3p 4.078473 4.104653 0.2058716 4.115271 4.122395 0.1680536 4.041675 4.049734 0.2327882 0.0735962 0.0735962 0.2444812 -0.0735962 -0.2444812 0.0086789 1.0000000 0.5380907 0.0137209
hsa.miR.484 1.597652 1.580193 0.2719205 1.550795 1.553409 0.1598979 1.644510 1.656175 0.3443530 -0.0937157 -0.0937157 -0.3113168 0.0937157 0.3113168 0.0116710 1.0000000 0.7119329 0.0182773
hsa.miR.452.5p 1.609759 1.684291 0.4772755 1.691423 1.719895 0.2895699 1.528095 1.619481 0.6003483 0.1633282 0.1633282 0.5425647 -0.1633282 -0.5425647 0.0122598 1.0000000 0.7355852 0.0189271
hsa.miR.584.5p 1.562512 1.609699 0.4055066 1.631695 1.617142 0.3258710 1.493330 1.570896 0.4632148 0.1383646 0.1383646 0.4596372 -0.1383646 -0.4596372 0.0123140 1.0000000 0.7355852 0.0189271
hsa.miR.9.5p 2.452682 2.417320 0.5298502 2.364790 2.362214 0.3600516 2.540574 2.612118 0.6472233 -0.1757844 -0.1757844 -0.5839430 0.1757844 0.5839430 0.0151165 1.0000000 0.8767577 0.0230215
hsa.miR.361.3p 2.114070 2.138671 0.2668813 2.157051 2.182644 0.1719882 2.071090 2.091288 0.3313815 0.0859613 0.0859613 0.2855574 -0.0859613 -0.2855574 0.0184170 1.0000000 1.0000000 0.0277930
hsa.let.7g.5p 2.743360 2.731598 0.2633678 2.701240 2.687710 0.2007329 2.785480 2.824734 0.3090374 -0.0842401 -0.0842401 -0.2798397 0.0842401 0.2798397 0.0191012 1.0000000 1.0000000 0.0285658
hsa.let.7a.3p 1.362918 1.456311 0.5840349 1.454096 1.472496 0.2172292 1.271740 1.413722 0.7883141 0.1823566 0.1823566 0.6057754 -0.1823566 -0.6057754 0.0227488 1.0000000 1.0000000 0.0337170
hsa.miR.28.3p 3.478699 3.452430 0.2371295 3.442283 3.445475 0.2164372 3.515115 3.488616 0.2519303 -0.0728325 -0.0728325 -0.2419443 0.0728325 0.2419443 0.0243409 1.0000000 1.0000000 0.0355939
hsa.miR.23b.3p 3.145549 3.139008 0.1654088 3.120156 3.106189 0.1396735 3.170942 3.185124 0.1848453 -0.0507862 -0.0507862 -0.1687082 0.0507862 0.1687082 0.0244440 1.0000000 1.0000000 0.0355939
hsa.miR.29b.3p 2.730065 2.739194 0.3702233 2.785646 2.771371 0.2357865 2.674484 2.713670 0.4621597 0.1111620 0.1111620 0.3692721 -0.1111620 -0.3692721 0.0281053 1.0000000 1.0000000 0.0405694

Let’s visualize the results of differential expression using heatmap and vulcano plot.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = F, margins = c(10, 10))

Z-scoring the values before clustering and plotting will help us to gain more insight.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = T, margins = c(10, 10))

We will also create a vulcano plot and label top 10 most significant miRNAs:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = sig_de$miR[1:10])

We may also what to check the consistency of differential expression between datasets:

de_test = OmicSelector_differential_expression_ttest(dplyr::select(test, starts_with("hsa")), test$Class)
de_valid = OmicSelector_differential_expression_ttest(dplyr::select(valid, starts_with("hsa")), valid$Class)
OmicSelector_correlation_plot(de$log2FC, de_test$log2FC, "log2FC on training set", "log2FC on test set", "", yx = T)

OmicSelector_correlation_plot(de$log2FC, de_valid$log2FC, "log2FC on training set", "log2FC on validation set", "", yx = T)

OmicSelector_correlation_plot(de_test$log2FC, de_valid$log2FC, "log2FC on test set", "log2FC on validation set", "", yx = T)

4 miRNA selection

The main feature of this package is the shotgun-like feature selection evaluation of possible miRNA signatures of biological processes. The function can be applied in a straightforward way, e.g.:

library(OmicSelector)
selected_features = OmicSelector_OmicSelector(wd = getwd(), m = c(1:3, 51), max_iterations = 1, stamp = "tutorial")  # For the sake of this tutorial and vignette building we will use only few fastest methods. The m parameter defines what methods will be tested. See more details below.

But, for largers projects we suggest using the following wrapper wich will perform the feature selection in parallel, significantly reducing computational time. We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing:

readLines("https://raw.githubusercontent.com/kstawiski/OmicSelector/master/vignettes/Tutorial_OmicSelector.R") %>% paste0(collapse = "\n") %>% cat
#> #options(warn = -1)
#> library(OmicSelector)
#> m = 1:56 # which methods to check?
#> 
#> 
#> # RECOMMENDED:
#> for (i in m) {
#> OmicSelector_OmicSelector(m = i, max_iterations = 1, stamp = "fs", debug = F, # we set debug to false (to make the package smaller), you may also want to change stamp to something meaningful, max_iterations was set to 1 to recude the computational time.. in real life scenarios it is resonable to use at least 10 iterations.
#>                   prefer_no_features = 11, # Few methods are filter rather than wrapper methods, thus requires the maximum number of maximum features.    
#>                   timeout_sec = 600) # We don't want to wait eternity in this tutorial, just 10 minutes. Timeout is useful for complicated methods. Depending on your CPU 2 days may be reasonable for larger projects. Note that some methods cannot be controled with timeout parameter.
#> }
#> 
#> # NOT RECOMMENDED: (due to huge computational load of some feature selection methods we do not recommend to run it in parallel, but it is possible)
#> suppressMessages(library(foreach))
#> suppressMessages(library(doParallel))
#> suppressMessages(library(parallel))
#> suppressMessages(library(doParallel))
#> cl <- makePSOCKcluster(useXDR = TRUE, 5) # We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing.
#>  registerDoParallel(cl)
#> # on.exit(stopCluster(cl))
#> iterations = length(m)
#> pb <- txtProgressBar(max = iterations, style = 3)
#> progress <- function(n) setTxtProgressBar(pb, n)
#> opts <- list(progress = progress)
#> foreach(i = m, .options.snow = opts) %dopar%
#> {
#>   suppressMessages(library(OmicSelector))
#>   # setwd("/OmicSelector/OmicSelector/vignettes") # change it you to your working directory
#>   OmicSelector_OmicSelector(m = i, max_iterations = 1, stamp = "tutorial", debug = F, # we set debug to false (to make the package smaller), you may also want to change stamp to something meaningful, max_iterations was set to 1 to recude the computational time.. in real life scenarios it is resonable to use at least 10 iterations.
#>                   prefer_no_features = 11, # Few methods are filter rather than wrapper methods, thus requires the maximum number of maximum features.
#>                   conda_path = "/opt/conda/bin/conda", # Methods line WxNet requires usage of python. In setup script we create conda enviorment. Providing conda_path makes it easier to activate env. We prefer this apporach over use_condaenv.
#>                   timeout = 600) # We don't want to wait eternity in this tutorial, just 10 minutes. Timeout is useful for complicated methods. Depending on your CPU 2 days may be reasonable for larger projects. Note that some methods cannot be controled with timeout parameter.
#> }
#> stopCluster(cl)

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

A few notes about what is does:

Files created for each method (e.g. for stamp=tutorial and m=1):

Pearls about the methods:

Notes about methods:

shiny::includeHTML("methods.html")
OmicSelector: Available methods of feature selection and benchmarking.

Contents

The main purpose of OmicSelector is to give you the set of candidate features for further validation of biomarker study. The package performs feature selection first. In the next step the sets of features are tested in the process called “benchmarking”. In benchmarking we test all of those sets of features (biomarkers) using various data-mining (machine learning) methods. Based on the avarage performance of sets in cross-validation or holdout-validation (testing on test set and/or validation set) we can sugesst which of the signitures (set of features) is have the greatest potential in further validation.

Please note that presented methods below are those avaiable in GUI (via web browser). Those can be further extended with ease by users with intermediate R knowledge. Please refer to our extension manuals (comming soon).

1 Feature selection methods

IDDescription
No: 1
all		 Get all features (all features staring with 'hsa').
No: 2
sig, sigtop, sigtopBonf, sigtopHolm, topFC, sigSMOTE, sigtopSMOTE, sigtopBonfSMOTE, sigtopHolmSMOTE, topFCSMOTE		 Selects features significantly differently expressed between classes by performing unpaired t-test with and without correction for multiple testing. We get: sig - all significant (adjusted p-value less or equal to 0.05) miRNAs with comparison using unpaired t-test and after the Benjamini-Hochberg procedure (BH, false discovery rate); sigtop - sig but limited only to the your prefered number of features (most significant features sorted by p-value), sigtopBonf - uses Bonferroni instead of BH correction, sigtopHolm - uses Holm–Bonferroni instead of BH correction, topFC - selects prefered number of features based on decreasing absolute value of fold change in differential analysis.
All the methods are also checked on dataset balanced with SMOTE (Synthetic Minority Oversampling TEchnique) - those formulas which names are appended with SMOTE.
No: 3
fcsig, fcsigSMOTE		 Features significant in DE analysis using unpaired t-test and which absolute log2FC is greater than 1. Thus, features significant and up- or down-regulated in the higher magnitudes. FC - fold-change, DE - differential analysis.
No: 4
cfs, cfsSMOTE, cfs_sig, cfsSMOTE_sig		 Correlation-based feature selection (CFS) - a heuristic algorithm selecting features that are highly correlated with class (binary) and lowly correlated with one another. It explores a search space in best-first manner, until stopping criteria are met.
No: 5
classloop		 Classifier loop - performs multiple classification procedures using various algorithms (with embedded feature ranking) and various performance metrices. Final feature selection is done by combining the results. Modeling methods used: support vector machines, linear discriminant a nalysis, random forest and nearest shrunken centroid. Features are selected based on the AUC ROC and assessed in k-fold cross-validation according to the documentation. As this requires time, we do not perform it on SMOTEd dataset.
No: 6
classloopSMOTE		 Application of classloop on balanced dataset (with SMOTE).
No: 7
classloop_sig		 Application of classloop but only on the features which are significant in DE.
No: 8
classloopSMOTE_sig		 Application of classloop on balanced training set and only on the features which are significant in DE (after balancing).
No: 9
fcfs		 An algorithm similar to CFS, though exploring search space in greedy forward search manner (adding one, most attractive, feature at the time, until such addition does not improve set’s overall quality). Based on Wang et al. 2005 and documented here.
No: 10
fcfsSMOTE		 Application of fcfs on balanced training set.
No: 11
fcfs_sig		 Application of fcfs on features significant in DE.
No: 12
fcfsSMOTE_sig		 Application of fcfs on balanced dataset and on features significant in DE (after balancing).
No: 13
fwrap		 A decision tree algorithm and forward search strategy documented here.
No: 14
fwrapSMOTE		 Application of fwrap on balanced training set.
No: 15
fwrap_sig		 Application of fwrap on features significant in DE.
No: 16
fwrapSMOTE_sig		 Application of fwrap on balanced dataset and on features significant in DE (after balancing).
No: 17
AUC_MDL		 Feature ranking based on ROC AUC and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below.
No: 18
SU_MDL		 Feature ranking based on symmetrical uncertainty and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below.
No: 19
CorrSF_MDL		 Feature ranking based on CFS algorithm with forward search and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below.
No: 20
AUC_MDLSMOTE		 Feature ranking based on ROC AUC and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE.
No: 21
SU_MDLSMOTE		 Feature ranking based on symmetrical uncertainty and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE.
No: 22
CorrSF_MDLSMOTE		 Feature ranking based on CFS algorithm with forward search and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE.
No: 23
AUC_MDL_sig		 Feature ranking based on ROC AUC and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Only features significant in DE are allowed.
No: 24
SU_MDL_sig		 Feature ranking based on symmetrical uncertainty and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Only features significant in DE are allowed.
No: 25
CorrSF_MDL_sig		 Feature ranking based on CFS algorithm with forward search and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Only features significant in DE are allowed.
No: 26
AUC_MDLSMOTE_sig		 Feature ranking based on ROC AUC and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE. Only features significant in DE are allowed.
No: 27
SU_MDLSMOTE_sig		 Feature ranking based on symmetrical uncertainty and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE. Only features significant in DE are allowed.
No: 28
CorrSF_MDLSMOTE_sig		 Feature ranking based on CFS algorithm with forward search and minimal description length (MDL) discretization algorithm documented here. After the ranking, the number of features are limited as set in options below. Performed on the training set balanced with SMOTE. Only features significant in DE are allowed.
No: 29
bounceR-full, bounceR-stability		 A component-wise-boosting-based algorithm selecting optimal features in multiple iterations of single feature-models construction. See the source here. bounceR-stability gets the most stable features. Wrapper methods implemented here leverage componentwise boosting as a weak learners.
No: 30
bounceR-full_SMOTE, bounceR-stability_SMOTE		 A component-wise-boosting-based algorithm selecting optimal features in multiple iterations of single feature-models construction. See the source here. bounceR-stability gets the most stable features. Wrapper methods implemented here leverage componentwise boosting as a weak learners. Performed on the training set balanced with SMOTE.
No: 31
bounceR-full_SIG, bounceR-stability_SIG		 A component-wise-boosting-based algorithm selecting optimal features in multiple iterations of single feature-models construction. See the source here. bounceR-stability gets the most stable features. Wrapper methods implemented here leverage componentwise boosting as a weak learners. Only features significant in DE are allowed.
No: 32
bounceR-full_SIGSMOTE, bounceR-stability_SIGSMOTE		 A component-wise-boosting-based algorithm selecting optimal features in multiple iterations of single feature-models construction. See the source here. bounceR-stability gets the most stable features. Wrapper methods implemented here leverage componentwise boosting as a weak learners. Only features significant in DE are allowed. Performed on the training set balanced with SMOTE.
No: 33
RandomForestRFE		 Recursively eliminates features from the feature space based on ranking from Random Forrest classifier (retrained woth resampling after each elimination). Details are available here.
No: 34
RandomForestRFESMOTE		 Recursively eliminates features from the feature space based on ranking from Random Forrest classifier (retrained woth resampling after each elimination). Details are available here. Performed on the training set balanced with SMOTE.
No: 35
RandomForestRFE_sig		 Recursively eliminates features from the feature space based on ranking from Random Forrest classifier (retrained woth resampling after each elimination). Details are available here. Only features significant in DE are allowed.
No: 36
RandomForestRFESMOTE_sig		 Recursively eliminates features from the feature space based on ranking from Random Forrest classifier (retrained woth resampling after each elimination). Details are available here. Only features significant in DE are allowed. Performed on the training set balanced with SMOTE.
No: 37
GeneticAlgorithmRF		 Uses genetic algorithm principle to search for optimal subset of the feature space. This uses internally implemented random forest model and 10-fold cross validation to assess performance of the "chromosomes" in each generation. Details are available here.
No: 38
GeneticAlgorithmRFSMOTE		 Uses genetic algorithm principle to search for optimal subset of the feature space. This uses internally implemented random forest model and 10-fold cross validation to assess performance of the "chromosomes" in each generation. Details are available here. Performed on the training set balanced with SMOTE.
No: 39
GeneticAlgorithmRF_sig		 Uses genetic algorithm principle to search for optimal subset of the feature space. This uses internally implemented random forest model and 10-fold cross validation to assess performance of the "chromosomes" in each generation. Details are available here. Only features significant in DE are allowed.
No: 40
GeneticAlgorithmRFSMOTE_sig		 Uses genetic algorithm principle to search for optimal subset of the feature space. This uses internally implemented random forest model and 10-fold cross validation to assess performance of the "chromosomes" in each generation. Details are available here. Only features significant in DE are allowed. Performed on the training set balanced with SMOTE.
No: 41
SimulatedAnnealingRF		 Simulated Annealing - explores a feature space by randomly modifying a given feature subset and evaluating classification performance using new attributes to check whether changes were beneficial. It is is a global search method that makes small random changes (i.e. perturbations) to an initial candidate solution. In this method also random forest is used as a model for evaluation. Details are available here.
No: 42
SimulatedAnnealingRFSMOTE		 Simulated Annealing - explores a feature space by randomly modifying a given feature subset and evaluating classification performance using new attributes to check whether changes were beneficial. It is is a global search method that makes small random changes (i.e. perturbations) to an initial candidate solution. In this method also random forest is used as a model for evaluation. Details are available here. Performed on the training set balanced with SMOTE.
No: 43
SimulatedAnnealingRF_sig		 Simulated Annealing - explores a feature space by randomly modifying a given feature subset and evaluating classification performance using new attributes to check whether changes were beneficial. It is is a global search method that makes small random changes (i.e. perturbations) to an initial candidate solution. In this method also random forest is used as a model for evaluation. Details are available here. Only features significant in DE are allowed.
No: 44
SimulatedAnnealingRFSMOTE_sig		 Simulated Annealing - explores a feature space by randomly modifying a given feature subset and evaluating classification performance using new attributes to check whether changes were beneficial. It is is a global search method that makes small random changes (i.e. perturbations) to an initial candidate solution. In this method also random forest is used as a model for evaluation. Details are available here. Only features significant in DE are allowed. Performed on the training set balanced with SMOTE.
No: 45
Boruta		 Boruta - utilizes random forrest algorithm to iteratively remove features proved to be less relevant than random variables. Details are available in paper by Kursa et al. 2010 or this blog post. Only features significant in DE are allowed. Performed on the training set balanced with SMOTE.
No: 46
BorutaSMOTE		 Boruta - utilizes random forrest algorithm to iteratively remove features proved to be less relevant than random variables. Details are available in paper by Kursa et al. 2010 or this blog post. Performed on the training set balanced with SMOTE.
No: 47
spFSR		 spFSR - feature selection and ranking by simultaneous perturbation stochastic approximation. This is an algorithm based on pseudo-gradient descent stochastic optimisation with Barzilai-Borwein method for step size and gradient estimation optimization. Details are available in paper by Zeren et al. 2018.
No: 48
spFSRSMOTE		 spFSR - feature selection and ranking by simultaneous perturbation stochastic approximation. This is an algorithm based on pseudo-gradient descent stochastic optimisation with Barzilai-Borwein method for step size and gradient estimation optimization. Details are available in paper by Zeren et al. 2018. Performed on the training set balanced with SMOTE.
No: 49
varSelRF, varSelRFSMOTE		 varSelRF - recursively eliminates features using random forrest feature scores, seeking to minimize out-of-bag classification error. Details are available in paper by Díaz-Uriarte et al. 2006. Performed on the unbalanced training set as well as on balanced with SMOTE.
No: 50
Wx, WxSMOTE		 Wx - deep neural network-based (deep learning) feature (gene) selection algorithm. We use 2 hidden layers with 16 hidden neurons. Details are available in paper by Park et al. 2019. Performed on the unbalanced training set as well as on balanced with SMOTE.
No: 51
Mystepwise_glm_binomial, Mystepwise_sig_glm_binomial		 Stepwise variable selection procedure (with iterations between the 'forward' and 'backward' steps) for generalized linear models with logit link function (i.e. logistic regression). We use p=0.05 as a threshold for both entry (SLE) and stay (SLS). Details are available here. Performed on all features of training set as well as features initially selected in DE (significant in DE).
No: 52
Mystepwise_glm_binomialSMOTE, Mystepwise_sig_glm_binomialSMOTE		 Stepwise variable selection procedure (with iterations between the 'forward' and 'backward' steps) for generalized linear models with logit link function (i.e. logistic regression). We use p=0.05 as a threshold for both entry (SLE) and stay (SLS). Details are available here. Performed on all features of training set as well as features initially selected in DE (significant in DE) after balancing the training set with SMOTE.
No: 53
stepAIC, stepAICsig		 Here we perform a stepwise model selection by AIC (Akaike Information Criterion) based on logistic regression. Details are available here. Performed on all features of training set as well as features initially selected in DE (significant in DE).
No: 54
stepAIC_SMOTE, stepAICsig_SMOTE		 Here we perform a stepwise model selection by AIC (Akaike Information Criterion) based on logistic regression. Details are available here. Performed on all features of training set as well as features initially selected in DE (significant in DE) after balancing the training set with SMOTE.
No: 55
iteratedRFECV, iteratedRFETest		 Iterated RFE tested in cross-validation and on test set (watch out for bias!). See the source here.
No: 56
iteratedRFECV_SMOTE, iteratedRFETest_SMOTE		 Iterated RFE tested in cross-validation and on test set (watch out for bias!). See the source here. Performed after balancing the training set with SMOTE.
Those methods can be applied via GUI or via OmicSelector_OmicSelector() function in the R package.

2 Benchmarking (data-minig modelling methods)

The GUI offers server data-mining algorithms which can be used in benchmarking:

IDDescription
glm Logistic regression (generalized linear model with binomial link function).
mlp Multilayer perceptron (MLP) - fully connected feedforward neural network with 1 hidden layer and logistic activiation function. Details: code, package.
mlpML Multilayer perceptron (MLP) - fully connected feedforward neural network with up to 3 hidden layers and logistic activiation function. Details: code, package.
svmRadial Support vector machines with radial basis function kernel. Details: code, package.
svmLinear Support vector machines with linear kernel. Details: code, package.
rf Random forest. Details: code, package.
C5.0 C5.0 decision trees and rule-based models. Details: code, package.
rpart CART decision trees with modulation of complexity parameter. Details: code, package.
rpart2 CART decision trees with modulation of max tree depth. Details: code, package.
ctree Conditional inference trees. Details: code, package.
mxnet MXNET-based deep neural networks up to 2 hidden layers, with multiple activation functions tested. Note that predefined grid search is used in hyperparameter optimization for this method (not random search). Details: code, package.
It uses early stopping with set by user maximum number of epochs.
xgbTree eXtreme gradient boosting. (note: this is a time-consuming method). Details: code, package.

However, the OmicSelector_benchmark() function works using caret, meaning that every model from the (caret list of methods)[https://topepo.github.io/caret/available-models.html] can be applied (assuming that the depending packages are installed; see the reference of OmicSelector_benchmark() for more details).

Note that the package performs the random search of hyperparameters. The best set of hyperparameters is chosen based on the performance on testing set (holdout validation) or strictly on training set (using cross-validation).

The OmicSelector functions saves all output files to temp/ directory. As users may want to run multiple selection methods in different configurations, we do not recommend using the return of this function in the following steps. Instead, we provide OmicSelector_merge_formulas() which conviniently summerizes the results of feature selection. We can do:

selected_sets_of_miRNAs = OmicSelector_merge_formulas(max_miRNAs = 11)  # we filter out sets with more than 11 miRNAs.
selected_sets_of_miRNAs_with_own = OmicSelector_merge_formulas(max_miRNAs = 11, add = list(my_own_signature = c("hsa.miR.192.5p", "hsa.let.7g.5p", "hsa.let.7a.5p", 
    "hsa.let.7d.5p", "hsa.miR.194.5p", "hsa.miR.98.5p", "hsa.let.7f.5p", "hsa.miR.26b.5p")))  # you can also add your own signature (for example selected from literature)

Note that:

Let’s analyze the process of feature selection:

all_sets = readRDS("featureselection_formulas_all.RDS")
length(all_sets)  # How many feature selection methods completed in time?
#> [1] 15
final_sets = readRDS("featureselection_formulas_final.RDS")
length(final_sets)  # How many feature selection methods completed in time and fulfilled max_miRNA criteria? (remember about fcsig and cfs_sig)
#> [1] 13
featureselection_formulas_final = fread("featureselection_formulas_final.csv")
OmicSelector_table(featureselection_formulas_final)  # show information about selected formulas
name formula ile_miRNA
my_own_signature Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p 0
sigtop Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
sigtopBonf Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
sigtopHolm Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p 11
sigtopSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
sigtopBonfSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
sigtopHolmSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p 11
fcsig Class ~ hsa.miR.375.3p + hsa.miR.217.5p 2
fcsigSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p 2
Mystepwise_glm_binomial Class ~ hsa.miR.21.5p + hsa.miR.130a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.146b.5p 6
Mystepwise_sig_glm_binomial Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p 6

Note that my_own_signture has 0 miRNAs according to the table. This trick is done to make sure that signatures added manually will not be filtered out based on max_miRNA parameter.

Now, we will summarize number of microRNAs selected by methods implemented in OmicSelector_OmicSelector by creating histogram and calculating some descriptive statistics.

hist(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)], breaks = ncol(train), main = "Number of selected microRNAs distribution", 
    xlab = "Number of selected microRNAs")  # Histogram showing how many miRNAs were selected in final set.

psych::describe(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)])  # Descriptive statistics of how many features where selected in the final set.
#>    vars  n mean   sd median trimmed mad min max range  skew kurtosis   se
#> X1    1 12 8.67 3.65     11     9.1   0   2  11     9 -0.91    -0.99 1.05

5 Benchmarking

In the next step of looking for the best microRNA signature, we perform benchmarking. This tests all the signatures using different classifier architectures. Here is the example of benchmark with default parameters:

readLines("Tutorial_benchmark.R") %>% paste0(collapse = "\n") %>% cat

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

Just for rendering this tutorial we will use a very simple benchmark using only logistic regression and conditional trees.

library(OmicSelector)
OmicSelector_tutorial_balanced_benchmark = OmicSelector_benchmark(search_iters = 5, # 5 random hyperparameter sets will be checked; 5 is set here for speed purposes.. for real projects use more, like 5000...
            algorithms = c("ctree"), # just add ctree, note that logistic regression (glm) is always included
            output_file = paste0("benchmark.csv")) # the main output
# exemplary benchmark data can be loaded using data('OmicSelector_tutorial_balanced_benchmark')

As benchmarking is done, the main result file is saved in file specified in output_file parameter. It contains the performance metrics of signatures satisfying initial criteria (e.g. max_miRNA) across different methods of modelling. Let’s take a quick look:

OmicSelector_table(fread("benchmark.csv"))
V1 method SMOTE miRy glm_modelname glm_train_ROCAUC glm_train_ROCAUC_lower95CI glm_train_ROCAUC_upper95CI glm_train_Accuracy glm_train_Sensitivity glm_train_Specificity glm_test_Accuracy glm_test_Sensitivity glm_test_Specificity glm_valid_Accuracy glm_valid_Sensitivity glm_valid_Specificity ctree_modelname ctree_train_ROCAUC ctree_train_ROCAUC_lower95CI ctree_train_ROCAUC_upper95CI ctree_train_Accuracy ctree_train_Sensitivity ctree_train_Specificity ctree_test_Accuracy ctree_test_Sensitivity ctree_test_Specificity ctree_valid_Accuracy ctree_valid_Sensitivity ctree_valid_Specificity
1 my_own_signature No Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p 1601119009 0.9239235 0.8901386 0.9577083 0.8317757 0.8504673 0.8130841 0.8472222 0.8055556 0.8888889 0.8857143 0.8857143 0.8857143 1601119215 0.9753254 0.9605664 0.9900843 0.8971963 0.8317757 0.9626168 0.7916667 0.6944444 0.8888889 0.8714286 0.8000000 0.9428571
2 sigtop No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1601119019 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1601119225 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
3 sigtopBonf No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1601119029 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1601119235 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
4 sigtopHolm No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1601119039 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1601119245 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
5 topFC No Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p 1601119049 0.9939733 0.9856621 1.0000000 0.9813084 0.9906542 0.9719626 0.9444444 1.0000000 0.8888889 0.9857143 1.0000000 0.9714286 1601119256 0.9944537 0.9893380 0.9995693 0.9579439 0.9906542 0.9252336 0.9305556 0.9722222 0.8888889 0.9714286 1.0000000 0.9428571
6 sigtopSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1601119061 0.9955128 0.9949946 0.9960310 0.9769842 0.9800000 0.9739983 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1601119267 0.9999625 0.9999424 0.9999826 0.9990236 1.0000000 0.9980568 0.8888889 0.8333333 0.9444444 0.9428571 0.8857143 1.0000000
7 sigtopBonfSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1601119086 0.9955128 0.9949946 0.9960310 0.9769842 0.9800000 0.9739983 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1601119291 0.9999625 0.9999424 0.9999826 0.9990236 1.0000000 0.9980568 0.8888889 0.8333333 0.9444444 0.9428571 0.8857143 1.0000000
8 sigtopHolmSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1601119110 0.9955128 0.9949946 0.9960310 0.9769842 0.9800000 0.9739983 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1601119316 0.9999625 0.9999424 0.9999826 0.9990236 1.0000000 0.9980568 0.8888889 0.8333333 0.9444444 0.9428571 0.8857143 1.0000000
9 topFCSMOTE Yes Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p 1601119134 0.9980829 0.9976736 0.9984922 0.9931185 1.0000000 0.9863052 0.9444444 1.0000000 0.8888889 0.9857143 1.0000000 0.9714286 1601119339 0.9998855 0.9997782 0.9999929 0.9990701 1.0000000 0.9981493 0.9722222 0.9444444 1.0000000 0.9571429 0.9142857 1.0000000
10 fcsig No Class ~ hsa.miR.375.3p + hsa.miR.217.5p 1601119156 0.9491659 0.9218955 0.9764362 0.8831776 0.8878505 0.8785047 0.8472222 0.9166667 0.7777778 0.8428571 0.8000000 0.8857143 1601119361 0.9692550 0.9508923 0.9876176 0.9018692 0.8691589 0.9345794 0.8333333 0.8611111 0.8055556 0.9142857 0.8285714 1.0000000
11 fcsigSMOTE Yes Class ~ hsa.miR.217.5p + hsa.miR.375.3p 1601119167 0.9584871 0.9561379 0.9608363 0.8971033 0.9028972 0.8913667 0.8611111 0.9444444 0.7777778 0.8428571 0.8000000 0.8857143 1601119372 0.9958044 0.9951857 0.9964232 0.9787976 1.0000000 0.9578051 0.8055556 0.7777778 0.8333333 0.8428571 0.7428571 0.9428571
12 Mystepwise_glm_binomial No Class ~ hsa.miR.21.5p + hsa.miR.130a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.146b.5p 1601119185 0.9995633 0.9987652 1.0000000 0.9906542 0.9906542 0.9906542 0.9583333 0.9722222 0.9444444 1.0000000 1.0000000 1.0000000 1601119392 0.9945410 0.9895576 0.9995244 0.9579439 0.9345794 0.9813084 0.9166667 0.9166667 0.9166667 0.9428571 0.9714286 0.9142857
13 Mystepwise_sig_glm_binomial No Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p 1601119195 0.9999127 0.9996706 1.0000000 0.9906542 0.9906542 0.9906542 0.9583333 1.0000000 0.9166667 1.0000000 1.0000000 1.0000000 1601119402 0.9888200 0.9767842 1.0000000 0.9532710 0.9532710 0.9532710 0.9583333 1.0000000 0.9166667 0.9428571 1.0000000 0.8857143

Description of columns:

By this logic every parameter is also calculated from testing (_test_) and validation (_valid_) set. If the method generated a probability, a default cutoff is used for all of the predictions.

Let’s see the general performance (accuracy) of methods in the benchmark:

metody = OmicSelector_get_benchmark_methods("benchmark.csv")  # gets the methods used in benchmark
par(mfrow = c(2, 2))
for (i in 1:length(metody)) {
    temp = OmicSelector_get_benchmark("benchmark.csv")  # loads benchmark
    temp2 = dplyr::select(temp, starts_with(paste0(metody[i], "_")))
    boxplot(temp[, paste0(metody[i], "_train_Accuracy")], temp[, paste0(metody[i], "_test_Accuracy")], temp[, paste0(metody[i], "_valid_Accuracy")], main = paste0("Method: ", 
        metody[i]), names = c("Training", "Testing", "Validation"), ylab = "Accuracy", ylim = c(0.5, 1))
    tempids = c(match(paste0(metody[i], "_train_Accuracy"), colnames(temp)), match(paste0(metody[i], "_test_Accuracy"), colnames(temp)), match(paste0(metody[i], 
        "_valid_Accuracy"), colnames(temp)))
}
par(mfrow = c(1, 1))

With OmicSelector package, the final optimal feature signature can be selected in 3 ways:

1. Picking the signture which achived the best accuracy in training, testing and validation: (metaindex = mean of all 3 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = F)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
topFCSMOTE 0.9752854 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
Mystepwise_sig_glm_binomial 0.9672415 Mystepwise_sig_glm_binomial Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p
topFC 0.9618992 topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p

2. Picking the signture which achived the best accuracy in testing and validation: (metaindex = mean of 2 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = T)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
topFCSMOTE 0.9648810 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
Mystepwise_sig_glm_binomial 0.9648810 Mystepwise_sig_glm_binomial Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p
topFC 0.9580357 topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p

3. The signture which achived the best sensitivity and specificity in validation: (metaindex = mean of sensivitiy and specificity in validation dataset)

acc = OmicSelector_best_signiture_proposals_meta11(benchmark_csv = "benchmark.csv")  # generates the benchmark sorted by metaindex
best_signatures = acc[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
topFC 0.9571429 topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
Mystepwise_sig_glm_binomial 0.9428571 Mystepwise_sig_glm_binomial Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p
topFCSMOTE 0.9428571 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

It is a good practice to assess learning performance for considered signatures across different classification methods. Here, we visualize the over/underfitting of selected methods by comparing accuracy score between testing and validation sets for 3 top scoring signatures across selection of model architectures.

for (i in 1:length(metody)) {
    suppressMessages(library(PairedData))
    suppressMessages(library(profileR))
    pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_test_Accuracy")]))
    colnames(pd) = c("Train Accuracy", "Test Accuracy")
    plot2 = OmicSelector_profileplot(pd, Method.id = acc$method[1:3], standardize = F)
    pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Train Accuracy", "Valid Accuracy")
    plot3 = OmicSelector_profileplot(pd, Method.id = acc$method[1:3], standardize = F)
    pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_test_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Test Accuracy", "Valid Accuracy")
    plot4 = OmicSelector_profileplot(pd, Method.id = acc$method[1:3], standardize = F)
    
    
    
    require(gridExtra)
    grid.arrange(arrangeGrob(plot2, plot3, ncol = 2, nrow = 1, top = metody[i]))
    grid.arrange(arrangeGrob(plot4, ncol = 1, nrow = 1, top = metody[i]))
}

The relationship betweend accuracy on testing and validation sets can also be pictured as scatterplot:

acc2 = acc[1:6, ]  # get top 6 methods
accmelt = melt(acc2, id.vars = "method") %>% filter(variable != "metaindex") %>% filter(variable != "miRy")
accmelt = cbind(accmelt, strsplit2(accmelt$variable, "_"))
acctest = accmelt$value[accmelt$`2` == "test"]
accvalid = accmelt$value[accmelt$`2` == "valid"]
accmeth = accmelt$method[accmelt$`2` == "test"]
unique(accmeth)
#> [1] "topFC"                       "Mystepwise_sig_glm_binomial"
#> [3] "topFCSMOTE"                  "Mystepwise_glm_binomial"    
#> [5] "sigtop"                      "sigtopBonf"
plot5 = ggplot(, aes(x = as.numeric(acctest), y = as.numeric(accvalid), shape = accmeth)) + geom_point() + scale_x_continuous(name = "Accuracy on test set", 
    limits = c(0.5, 1)) + scale_y_continuous(name = "Accuracy on validation set", limits = c(0.5, 1)) + theme_bw()
grid.arrange(arrangeGrob(plot5, ncol = 1, nrow = 1))

6 Best signture analysis

Suppose we decide to use sensitivity and specificity in validation set (e.g. in the model architectures we plan to use in our research) as decisive scoring metric for feature signature. The three best signatures may be:

OmicSelector_table(best_signatures[1:3, 2:4])
method SMOTE miRy
topFC topFC No Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
Mystepwise_sig_glm_binomial Mystepwise_sig_glm_binomial No Class ~ hsa.miR.21.5p + hsa.miR.26b.5p + hsa.miR.30c.2.3p + hsa.miR.375.3p + hsa.miR.378a.3p + hsa.miR.338.3p
topFCSMOTE topFCSMOTE Yes Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

To get the miRNAs from formula you can use OmicSelector_get_features_from_benchmark.

selected_miRNAs = OmicSelector_get_features_from_benchmark(benchmark_csv = "benchmark.csv", best_signatures$method[1])  # for the best performing signiture
gsub("\\.", "-", selected_miRNAs)  # R doesn't like hyphens, but we can introduce them easly
#>  [1] "hsa-miR-217-5p"  "hsa-miR-375-3p"  "hsa-miR-192-5p"  "hsa-miR-194-5p" 
#>  [5] "hsa-miR-21-5p"   "hsa-miR-30a-3p"  "hsa-miR-199b-5p" "hsa-miR-200a-3p"
#>  [9] "hsa-miR-708-3p"  "hsa-miR-144-5p"  "hsa-miR-141-3p"

As a double check, we can inspect the differential expression of miRNAs constituating selected signature:

best_de = OmicSelector_best_signiture_de(selected_miRNAs)
OmicSelector_table(best_de)
miR log2FC p-value p-value BH
7 hsa.miR.217.5p 4.996853 0 0
6 hsa.miR.375.3p 4.788105 0 0
23 hsa.miR.192.5p 2.963697 0 0
18 hsa.miR.194.5p 2.943915 0 0
1 hsa.miR.21.5p 2.602216 0 0
3 hsa.miR.30a.3p -2.441965 0 0
11 hsa.miR.199b.5p 2.381457 0 0
25 hsa.miR.200a.3p 2.194942 0 0
30 hsa.miR.708.3p 2.162216 0 0
39 hsa.miR.144.5p -2.112787 0 0
26 hsa.miR.141.3p 2.108966 0 0

Let’s visualize the performance of those methods using barplots:

for (i in 1:3) {
    cat(paste0("\n\n## ", acc$method[i], "\n\n"))
    par(mfrow = c(1, 2))
    acc = OmicSelector_best_signiture_proposals_meta11("benchmark.csv")
    metody = OmicSelector_get_benchmark_methods("benchmark.csv")
    ktory_set = match(acc$method[i], OmicSelector_get_benchmark("benchmark.csv")$method)
    # do_ktorej_kolumny = which(colnames(acc) == 'metaindex') barplot(as.numeric(acc[i,1:do_ktorej_kolumny]))
    for (ii in 1:length(metody)) {
        
        temp = OmicSelector_get_benchmark("benchmark.csv") %>% dplyr::select(starts_with(paste0(metody[ii], "_t")), starts_with(paste0(metody[ii], "_v")))
        
        ROCtext = paste0("Training AUC ROC: ", round(temp[ktory_set, 1], 2), " (95%CI: ", round(temp[ktory_set, 2], 2), "-", round(temp[ktory_set, 3], 
            2), ")")
        
        temp = temp[, -c(1:3)]
        temp2 = as.numeric(temp[ktory_set, ])
        temp3 = matrix(temp2, nrow = 3, byrow = T)
        colnames(temp3) = c("Accuracy", "Sensitivity", "Specificity")
        rownames(temp3) = c("Training", "Testing", "Validation")
        temp3 = t(temp3)
        
        plot1 = barplot(temp3, beside = T, ylim = c(0, 1), xlab = paste0(ROCtext, "\nBlack - accuracy, blue - sensitivity, green - specificity"), width = 0.85, 
            col = c("black", "blue", "green"), legend = F, args.legend = list(x = "topright", bty = "n", inset = c(0, -0.25)), cex.lab = 0.7, main = paste0(acc$method[i], 
                " - ", metody[ii]), font.lab = 2)
        ## Add text at top of bars
        text(x = plot1, y = as.numeric(temp3), label = paste0(round(as.numeric(temp[ktory_set, ]) * 100, 1), "%"), pos = 3, cex = 0.6, col = "red")
    }
    par(mfrow = c(1, 1))
    
}
#> 
#> 
#> ## topFC

#> 
#> 
#> ## Mystepwise_sig_glm_binomial

#> 
#> 
#> ## topFCSMOTE

Finally, we can assess the overlap of top 3 feature selection methods:

overlap = OmicSelector_signiture_overlap(acc$method[1:3], "benchmark.csv")

Which miRNAs are common for between feature selection methods?

attr(overlap, "intersections")
#> $topFCSMOTE
#> [1] "hsa.miR.210.3p"
#> 
#> $`topFC:topFCSMOTE`
#> [1] "hsa.miR.217.5p"  "hsa.miR.192.5p"  "hsa.miR.194.5p"  "hsa.miR.30a.3p" 
#> [5] "hsa.miR.199b.5p" "hsa.miR.200a.3p" "hsa.miR.144.5p" 
#> 
#> $Mystepwise_sig_glm_binomial
#> [1] "hsa.miR.26b.5p"  "hsa.miR.378a.3p" "hsa.miR.338.3p" 
#> 
#> $`Mystepwise_sig_glm_binomial:topFCSMOTE`
#> [1] "hsa.miR.30c.2.3p"
#> 
#> $`topFC:Mystepwise_sig_glm_binomial:topFCSMOTE`
#> [1] "hsa.miR.375.3p" "hsa.miR.21.5p" 
#> 
#> $topFC
#> [1] "hsa.miR.708.3p" "hsa.miR.141.3p"

Let’s draw vulcano plot and mark the miRNAs selected in best signature:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = selected_miRNAs)

Let’s draw heatmap for selected miRNAs in whole dataset (training, testing and validation set).

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = F, margins = c(10, 
    10))

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = T, margins = c(10, 
    10))

Based on everything we have done so far, we suggest using the following signiture in further validation of biomarker study.

cat(paste0(gsub("\\.", "-", selected_miRNAs), collapse = ", "))
#> hsa-miR-217-5p, hsa-miR-375-3p, hsa-miR-192-5p, hsa-miR-194-5p, hsa-miR-21-5p, hsa-miR-30a-3p, hsa-miR-199b-5p, hsa-miR-200a-3p, hsa-miR-708-3p, hsa-miR-144-5p, hsa-miR-141-3p

7 Sesssion

session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Ubuntu 18.04.4 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language (EN)                        
#>  collate  C                           
#>  ctype    en_US.UTF-8                 
#>  tz       Europe/Warsaw               
#>  date     2020-09-26                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package              * version    date       lib
#>    abind                  1.4-5      2016-07-21 [2]
#>    annotate               1.66.0     2020-04-27 [2]
#>    AnnotationDbi          1.50.1     2020-06-29 [2]
#>    arules                 1.6-6      2020-05-15 [2]
#>    askpass                1.1        2019-01-13 [2]
#>    assertthat             0.2.1      2019-03-21 [2]
#>    backports              1.1.8      2020-06-17 [2]
#>    base64enc              0.1-3      2015-07-28 [2]
#>    BBmisc                 1.11       2017-03-10 [2]
#>    Biobase                2.48.0     2020-04-27 [2]
#>    BiocFileCache          1.12.0     2020-04-27 [2]
#>    BiocGenerics           0.34.0     2020-04-27 [2]
#>    BiocManager            1.30.10    2019-11-16 [1]
#>    Biocomb              * 0.4        2018-05-18 [2]
#>    BiocParallel           1.22.0     2020-04-27 [2]
#>    BiocStyle            * 2.16.0     2020-04-27 [1]
#>    biomaRt                2.44.1     2020-06-17 [2]
#>    Biostrings             2.56.0     2020-04-27 [2]
#>    bit                    1.1-15.2   2020-02-10 [2]
#>    bit64                  0.9-7.1    2020-07-15 [2]
#>    bitops                 1.0-6      2013-08-17 [2]
#>    blob                   1.2.1      2020-01-20 [2]
#>    bookdown               0.20       2020-06-23 [2]
#>    boot                   1.3-25     2020-04-26 [2]
#>    Boruta                 7.0.0      2020-05-21 [2]
#>    broom                  0.7.0      2020-07-09 [2]
#>    C50                  * 0.1.3.1    2020-05-26 [2]
#>    calibrate              1.7.7      2020-06-19 [2]
#>    callr                  3.4.3      2020-03-28 [2]
#>    car                    3.0-8      2020-05-21 [2]
#>    carData                3.0-4      2020-05-22 [2]
#>    caret                * 6.0-86     2020-03-20 [2]
#>    caTools                1.18.0     2020-01-17 [2]
#>    cellranger             1.1.0      2016-07-27 [2]
#>    checkmate              2.0.0      2020-02-06 [2]
#>    circlize               0.4.10     2020-06-15 [2]
#>    class                  7.3-17     2020-04-26 [2]
#>    classInt             * 0.4-3      2020-04-07 [2]
#>    cli                    2.0.2      2020-02-28 [2]
#>    clue                   0.3-57     2019-02-25 [2]
#>    cluster                2.1.0      2019-06-19 [2]
#>    clusterProfiler        3.16.0     2020-04-27 [2]
#>    codetools              0.2-16     2018-12-24 [2]
#>    coin                   1.3-1      2019-08-28 [2]
#>    colorspace             1.4-1      2019-03-18 [2]
#>    ComplexHeatmap         2.4.2      2020-05-04 [2]
#>    cowplot                1.0.0      2019-07-11 [2]
#>    crayon                 1.3.4      2017-09-16 [2]
#>    crosstalk              1.1.0.1    2020-03-13 [2]
#>    Cubist                 0.2.3      2020-01-10 [2]
#>    curl                   4.3        2019-12-02 [2]
#>    cutpointr              1.0.32     2020-06-19 [2]
#>    data.table           * 1.12.8     2019-12-09 [2]
#>    DBI                    1.1.0      2019-12-15 [2]
#>    dbplyr                 1.4.4      2020-05-27 [2]
#>    deepnet                0.2        2014-03-20 [2]
#>    DelayedArray           0.14.1     2020-07-14 [2]
#>    DEoptimR               1.0-8      2016-11-19 [2]
#>    desc                   1.2.0      2018-05-01 [2]
#>    DESeq2                 1.28.1     2020-05-12 [2]
#>    devtools             * 2.3.0      2020-04-10 [2]
#>    digest                 0.6.25     2020-02-23 [2]
#>    DMwR                 * 0.4.1      2013-08-08 [2]
#>    DO.db                  2.9        2020-05-31 [2]
#>    doParallel           * 1.0.15     2019-08-02 [2]
#>    DOSE                   3.14.0     2020-04-27 [2]
#>    downloader             0.4        2015-07-09 [2]
#>    dplyr                * 1.0.0      2020-05-29 [2]
#>    DT                     0.14       2020-06-24 [2]
#>    e1071                  1.7-3      2019-11-26 [2]
#>    edgeR                * 3.30.3     2020-06-02 [2]
#>    ellipsis               0.3.1      2020-05-15 [2]
#>    enrichplot             1.8.1      2020-04-29 [2]
#>    entropy                1.2.1      2014-11-14 [2]
#>    epiDisplay           * 3.5.0.1    2018-05-10 [2]
#>    europepmc              0.4        2020-05-31 [2]
#>    evaluate               0.14       2019-05-28 [2]
#>    fansi                  0.4.1      2020-01-08 [2]
#>    farver                 2.0.3      2020-01-16 [2]
#>    fastmap                1.0.1      2019-10-08 [2]
#>    fastmatch              1.1-0      2017-01-28 [2]
#>    fgsea                  1.14.0     2020-04-27 [2]
#>    forcats              * 0.5.0      2020-03-01 [2]
#>    foreach              * 1.5.0      2020-03-30 [2]
#>    foreign              * 0.8-80     2020-05-24 [2]
#>    formatR                1.7        2019-06-11 [2]
#>    Formula                1.2-3      2018-05-03 [2]
#>    fs                     1.4.2      2020-06-30 [2]
#>    FSelector              0.31       2018-05-16 [2]
#>    futile.logger          1.4.3      2016-07-10 [2]
#>    futile.options         1.0.1      2018-04-20 [2]
#>    gdata                  2.18.0     2017-06-06 [2]
#>    GDCRNATools            1.8.0      2020-04-27 [2]
#>    genefilter             1.70.0     2020-04-27 [2]
#>    geneplotter            1.66.0     2020-04-27 [2]
#>    generics               0.0.2      2018-11-29 [2]
#>    GenomeInfoDb           1.24.2     2020-06-15 [2]
#>    GenomeInfoDbData       1.2.3      2020-05-28 [2]
#>    GenomicDataCommons     1.12.0     2020-04-27 [2]
#>    GenomicRanges          1.40.0     2020-04-27 [2]
#>    GetoptLong             1.0.2      2020-07-06 [2]
#>    ggbiplot             * 0.55       2020-05-31 [2]
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#>    ggplot2              * 3.3.2      2020-06-19 [2]
#>    ggplotify              0.0.5      2020-03-12 [2]
#>    ggpubr                 0.4.0      2020-06-27 [2]
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#>    ggridges               0.5.2      2020-01-12 [2]
#>    ggsignif               0.6.0      2019-08-08 [2]
#>    gld                  * 2.6.2      2020-01-08 [2]
#>    GlobalOptions          0.1.2      2020-06-10 [2]
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#>    GO.db                  3.11.4     2020-05-28 [2]
#>    GOSemSim               2.14.0     2020-04-27 [2]
#>    gower                  0.2.2      2020-06-23 [2]
#>    gplots               * 3.0.4      2020-07-05 [2]
#>    graph                  1.66.0     2020-04-27 [2]
#>    graphlayouts           0.7.0      2020-04-25 [2]
#>    gridExtra            * 2.3        2017-09-09 [2]
#>    gridGraphics           0.5-0      2020-02-25 [2]
#>    gtable                 0.3.0      2019-03-25 [2]
#>    gtools               * 3.8.2      2020-03-31 [2]
#>    haven                  2.3.1      2020-06-01 [2]
#>    highr                  0.8        2019-03-20 [2]
#>    hms                    0.5.3      2020-01-08 [2]
#>    htmltools              0.5.0      2020-06-16 [2]
#>    htmlwidgets            1.5.1      2019-10-08 [2]
#>    httpuv                 1.5.4      2020-06-06 [2]
#>    httr                   1.4.2      2020-07-20 [2]
#>    igraph                 1.2.5      2020-03-19 [2]
#>    imputeMissings         0.0.3      2016-09-06 [2]
#>    inum                   1.0-1      2019-04-25 [2]
#>    ipred                  0.9-9      2019-04-28 [2]
#>    IRanges                2.22.2     2020-05-21 [2]
#>    iterators            * 1.0.12     2019-07-26 [2]
#>    jsonlite               1.7.0      2020-06-25 [2]
#>    kableExtra           * 1.1.0      2019-03-16 [2]
#>    KEGGgraph              1.48.0     2020-04-27 [2]
#>    KEGGREST               1.28.0     2020-04-27 [2]
#>    keras                  2.3.0.0    2020-05-19 [2]
#>    kernlab                0.9-29     2019-11-12 [2]
#>    KernSmooth             2.23-17    2020-04-26 [2]
#>    km.ci                  0.5-2      2009-08-30 [2]
#>    KMsurv                 0.1-5      2012-12-03 [2]
#>    knitr                * 1.29       2020-06-23 [2]
#>    labeling               0.3        2014-08-23 [2]
#>    laeken                 0.5.1      2020-02-05 [2]
#>    lambda.r               1.2.4      2019-09-18 [2]
#>    later                  1.1.0.1    2020-06-05 [2]
#>    lattice              * 0.20-41    2020-04-02 [2]
#>    lava                   1.6.7      2020-03-05 [2]
#>    lavaan               * 0.6-6      2020-05-13 [2]
#>    lazyeval               0.2.2      2019-03-15 [2]
#>    libcoin                1.0-5      2019-08-27 [2]
#>    lifecycle              0.2.0      2020-03-06 [2]
#>    limma                * 3.44.3     2020-06-12 [2]
#>    lme4                   1.1-23     2020-04-07 [2]
#>    lmom                   2.8        2019-03-12 [2]
#>    lmtest                 0.9-37     2019-04-30 [2]
#>    locfit                 1.5-9.4    2020-03-25 [2]
#>    lubridate              1.7.9      2020-06-08 [2]
#>    magick                 2.4.0      2020-06-23 [2]
#>    magrittr               1.5        2014-11-22 [2]
#>    manipulateWidget       0.10.1     2020-02-24 [2]
#>    MASS                 * 7.3-51.6   2020-04-26 [2]
#>    MatchIt              * 3.0.2      2018-01-09 [2]
#>    Matrix                 1.2-18     2019-11-27 [2]
#>    matrixStats            0.56.0     2020-03-13 [2]
#>    memoise                1.1.0      2017-04-21 [2]
#>    mgcv                   1.8-31     2019-11-09 [2]
#>    mice                 * 3.10.0     2020-07-13 [2]
#>    mime                   0.9        2020-02-04 [2]
#>    miniUI                 0.1.1.1    2018-05-18 [2]
#>    minqa                  1.2.4      2014-10-09 [2]
#>  P OmicSelector        * 0.1.0      2020-09-26 [?]
#>    mlr                    2.17.1     2020-03-24 [2]
#>    mnormt                 2.0.1      2020-06-29 [1]
#>    ModelMetrics           1.2.2.2    2020-03-17 [2]
#>    modelr                 0.1.8      2020-05-19 [2]
#>    modeltools             0.2-23     2020-03-05 [2]
#>    multcomp               1.4-13     2020-04-08 [2]
#>    munsell                0.5.0      2018-06-12 [2]
#>    mvtnorm              * 1.1-1      2020-06-09 [2]
#>    My.stepwise          * 0.1.0      2017-06-29 [2]
#>    naniar                 0.5.2      2020-06-29 [2]
#>    networkD3              0.4        2017-03-18 [2]
#>    nlme                   3.1-148    2020-05-24 [2]
#>    nloptr                 1.2.2.2    2020-07-02 [2]
#>    nnet                 * 7.3-14     2020-04-26 [2]
#>    numDeriv               2016.8-1.1 2019-06-06 [2]
#>    openssl                1.4.2      2020-06-27 [2]
#>    openxlsx               4.1.5      2020-05-06 [2]
#>    org.Hs.eg.db           3.11.4     2020-05-28 [2]
#>    PairedData           * 1.1.1      2018-06-02 [2]
#>    pamr                   1.56.1     2019-04-22 [2]
#>    parallelMap            1.5.0      2020-03-26 [2]
#>    ParamHelpers           1.14       2020-03-24 [2]
#>    party                  1.3-5      2020-06-12 [2]
#>    partykit               1.2-9      2020-07-10 [2]
#>    pathview               1.28.1     2020-07-19 [2]
#>    pbivnorm               0.6.0      2015-01-23 [2]
#>    pillar                 1.4.6      2020-07-10 [2]
#>    pkgbuild               1.1.0      2020-07-13 [2]
#>    pkgconfig              2.0.3      2019-09-22 [2]
#>    pkgload                1.1.0      2020-05-29 [2]
#>    plotly               * 4.9.2.1    2020-04-04 [2]
#>    plyr                 * 1.8.6      2020-03-03 [2]
#>    png                    0.1-7      2013-12-03 [2]
#>    polyclip               1.10-0     2019-03-14 [2]
#>    prettyunits            1.1.1      2020-01-24 [2]
#>    pROC                 * 1.16.2     2020-03-19 [2]
#>    processx               3.4.3      2020-07-05 [2]
#>    prodlim                2019.11.13 2019-11-17 [2]
#>    profileR             * 0.3-5      2018-04-19 [2]
#>    progress               1.2.2      2019-05-16 [2]
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#>    purrr                * 0.3.4      2020-04-17 [2]
#>    quantmod               0.4.17     2020-03-31 [2]
#>    qvalue                 2.20.0     2020-04-27 [2]
#>    R.methodsS3          * 1.8.0      2020-02-14 [2]
#>    R.oo                 * 1.23.0     2019-11-03 [2]
#>    R.utils              * 2.9.2      2019-12-08 [2]
#>    R6                     2.4.1      2019-11-12 [2]
#>    randomForest         * 4.6-14     2018-03-25 [2]
#>    ranger                 0.12.1     2020-01-10 [2]
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#>    Rcpp                 * 1.0.5      2020-07-06 [2]
#>    RCurl                  1.98-1.2   2020-04-18 [2]
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#>    remotes              * 2.2.0      2020-07-21 [2]
#>    reprex                 0.3.0      2019-05-16 [2]
#>    reshape              * 0.8.8      2018-10-23 [2]
#>    reshape2               1.4.4      2020-04-09 [2]
#>    reticulate           * 1.16       2020-05-27 [2]
#>    rgl                    0.100.54   2020-04-14 [2]
#>    Rgraphviz              2.32.0     2020-04-27 [2]
#>    rio                    0.5.16     2018-11-26 [2]
#>    rJava                  0.9-13     2020-07-06 [2]
#>    rjson                  0.2.20     2018-06-08 [2]
#>    rlang                  0.4.7      2020-07-09 [2]
#>    rmarkdown            * 2.3        2020-06-18 [2]
#>    robustbase             0.93-6     2020-03-23 [2]
#>    ROCR                   1.0-11     2020-05-02 [2]
#>    ROSE                 * 0.0-3      2014-07-15 [2]
#>    roxygen2               7.1.1      2020-06-27 [2]
#>    rpart                  4.1-15     2019-04-12 [2]
#>    rprojroot              1.3-2      2018-01-03 [2]
#>    RSNNS                  0.4-12     2019-09-17 [2]
#>    rsq                  * 2.0        2020-05-09 [2]
#>    RSQLite                2.2.0      2020-01-07 [2]
#>    rstatix                0.6.0      2020-06-18 [2]
#>    rstudioapi             0.11       2020-02-07 [2]
#>    rvcheck                0.1.8      2020-03-01 [2]
#>    rvest                  0.3.5      2019-11-08 [2]
#>    RWeka                  0.4-42     2020-02-02 [2]
#>    RWekajars              3.9.3-2    2019-10-19 [2]
#>    S4Vectors              0.26.1     2020-05-16 [2]
#>    sandwich               2.5-1      2019-04-06 [2]
#>    scales               * 1.1.1      2020-05-11 [2]
#>    scatterpie             0.1.4      2019-11-08 [2]
#>    sessioninfo            1.1.1      2018-11-05 [2]
#>    shape                  1.4.4      2018-02-07 [2]
#>    shiny                  1.5.0      2020-06-23 [2]
#>    snow                   0.4-3      2018-09-14 [2]
#>    sp                     1.4-2      2020-05-20 [2]
#>    spFSR                  1.0.0      2018-05-11 [2]
#>    stargazer            * 5.2.2      2018-05-30 [2]
#>    statmod                1.4.34     2020-02-17 [2]
#>    stringi                1.4.6      2020-02-17 [2]
#>    stringr              * 1.4.0      2019-02-10 [2]
#>    strucchange            1.5-2      2019-10-12 [2]
#>    SummarizedExperiment   1.18.2     2020-07-09 [2]
#>    survival             * 3.2-3      2020-06-13 [2]
#>    survminer              0.4.7      2020-05-28 [2]
#>    survMisc               0.5.5      2018-07-05 [2]
#>    sva                    3.36.0     2020-04-27 [2]
#>    TCGAbiolinks           2.16.3     2020-07-15 [2]
#>    tensorflow             2.2.0      2020-05-11 [2]
#>    testthat               2.3.2      2020-03-02 [2]
#>    tfruns                 1.4        2018-08-25 [2]
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#> 
#> [1] /home/konrad/R/x86_64-pc-linux-gnu-library/4.0
#> [2] /usr/lib/R/site-library
#> [3] /usr/lib/R/library
#> 
#>  P ── Loaded and on-disk path mismatch.
packageDescription("OmicSelector")
#> Package: OmicSelector
#> Type: Package
#> Title: OmicSelector - a package for biomarker miRNA selection based on
#>         miRNA-seq NGS data.
#> Version: 0.1.0
#> Author: Konrad Stawiski
#> Maintainer: Konrad Stawiski <konrad@konsta.com.pl>
#> Description: OmicSelector is package is the environment, docker-based
#>         application and R package for biomarker signiture selection
#>         from high-throughput experiments. Initially developed for
#>         miRNA-seq. The package introduces automatic and structured
#>         feature selection with further benchmarking using multiple data
#>         mining methods, thus allow to find the most overfitting
#>         resiliant signiture (set of featrues) that can be used in
#>         biomarker validation studies. E.g. this package can be used to
#>         find the set of miRNAs with the greatest biomarker potential
#>         based on miRNAs-seq. This set can be further validated in
#>         cheaper qPCR studies.
#> License: License: MIT + file LICENSE
#> Encoding: UTF-8
#> LazyData: true
#> Suggests: knitr, rmarkdown
#> VignetteBuilder: knitr
#> StagedInstall: yes
#> Imports: dplyr, snow, remotes, devtools, ellipsis, BiocManager, plyr,
#>         tibble, tidyr, XML, epiDisplay, rsq, MASS, caret, tidyverse,
#>         xtable, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr,
#>         data.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise,
#>         psych, C50, randomForest, nnet, reticulate, stargazer, ggrepel,
#>         classInt, plotly, keras, cutpointr, naniar, visdat,
#>         imputeMissings, foreach, deepnet, calibrate, networkD3,
#>         VennDiagram, RSNNS, kernlab, car, PairedData, profileR,
#>         xgboost, kableExtra, curl, tidyselect, rJava, mice, MatchIt,
#>         cluster, Biobase, Biocomb, ComplexHeatmap, GDCRNATools,
#>         R.utils, TCGAbiolinks, VIM, circlize, edgeR, magick, mgcv,
#>         party, rmarkdown, rpart, sva, devtools, nnet
#> RoxygenNote: 7.1.1
#> Authors@R: c( person("Konrad", "Stawiski", , "konrad@konsta.com.pl",
#>         role = c("aut", "cre"), comment = c(ORCID =
#>         "0000-0002-6550-3384") ), person("Marcin", "Kaszkowiak", role =
#>         "aut"))
#> BugReports: https://github.com/kstawiski/OmicSelector/issues
#> URL: https://kstawiski.github.io/OmicSelector/
#> biocViews: Software
#> Depends: R (>= 2.10)
#> 
#> -- File: /home/konrad/snorlax/OmicSelector/DESCRIPTION

To render this tutorial we used:

render("Tutorial.Rmd", output_file = "Tutorial.html", output_dir = "../inst/doc/")

Packages installed in our docker enviorment:

OmicSelector_table(as.data.frame(installed.packages()))
Package LibPath Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use OS_type MD5sum NeedsCompilation Built
BiocManager BiocManager /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 1.30.10 NA NA utils NA BiocStyle, BiocVersion, remotes, testthat, withr, curl, knitr NA Artistic-2.0 NA NA NA NA no 4.0.2
BiocStyle BiocStyle /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 2.16.0 NA NA bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager NA BiocGenerics, RUnit, htmltools NA Artistic-2.0 NA NA NA NA no 4.0.2
MLeval MLeval /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.3 NA R (>= 3.5.0) ggplot2 NA knitr, rmarkdown NA AGPL-3 NA NA NA NA no 4.0.0
RVAideMemoire RVAideMemoire /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.9-77 NA NA ade4 (>= 1.7-8), boot, car, FactoMineR, graphics, grDevices, lme4 (>= 1.0-4), MASS, mixOmics, nnet, pls, pspearman, stats, utils, vegan (>= 2.4-3) NA dgof, emmeans, ordinal, survival NA GPL-2 NA NA NA NA no 4.0.0
Rmisc Rmisc /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 1.5 NA lattice, plyr NA NA latticeExtra, Hmisc, stats4 NA GPL-3 NA NA NA NA no 4.0.2
TMB TMB /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 1.7.18 NA R (>= 3.0.0) graphics, methods, stats, utils, Matrix (>= 1.0-12) Matrix, RcppEigen numDeriv, parallel NA GPL-2 NA NA NA NA yes 4.0.2
biostatUZH biostatUZH /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 1.8.0 NA R (>= 2.15.0), grDevices, graphics, stats, survival (>= 2.35) boot NA cmprsk, lme4, prodlim, psy, xtable, reporttools, Hmisc, surveillance, carData MASS, ellipse GPL (>=2) NA NA NA NA no 4.0.0
broom.mixed broom.mixed /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.2.6 NA NA broom, dplyr, tidyr, plyr, purrr, tibble, reshape2, nlme, methods, stringr, coda, TMB, cubelyr NA knitr, testthat, ggplot2, Matrix, MCMCglmm, lme4, brms, mgcv, gamlss, gamlss.data, lmerTest, pbkrtest, glmmADMB, glmmTMB, dotwhisker, pander, R2jags, GLMMadaptive, rstan, rstanarm NA GPL-3 NA NA NA NA no 4.0.2
cpp11 cpp11 /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.2.1 NA NA NA NA bench, brio, callr, cli, covr, decor, desc, ggplot2, glue, knitr, lobstr, mockery, progress, rmarkdown, scales, testthat, tibble, utils, vctrs, withr NA MIT + file LICENSE NA NA NA NA no 4.0.2
cr17 cr17 /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.1.0 NA ggplot2 (>= 2.2.1), survival (>= 2.41-3), cmprsk (>= 2.2-7), gridExtra (>= 2.2.1), R (>= 3.3.2) dplyr (>= 0.5.0), scales (>= 0.4.1), grid (>= 3.3.0), gtable (>= 0.2.0) NA knitr, rmarkdown NA GPL NA NA NA NA no 4.0.0
cubelyr cubelyr /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 1.0.0 NA R (>= 3.2) dplyr, glue, pillar, purrr, rlang, tibble, tidyselect NA covr, testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA no 4.0.2
ezfun ezfun /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.1.3 NA R (>= 3.1.0) NA NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 4.0.0
gmodels gmodels /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 2.18.1 NA R (>= 1.9.0) MASS, gdata NA gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0) NA GPL-2 NA NA NA NA no 4.0.2
gt gt /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 0.2.2 NA R (>= 3.2.0) checkmate (>= 2.0.0), commonmark (>= 1.7), dplyr (>= 0.8.5), fs (>= 1.3.2), ggplot2 (>= 3.3.0), glue (>= 1.3.2), htmltools (>= 0.5.0), magrittr (>= 1.5), rlang (>= 0.4.5), sass (>= 0.1.1), scales (>= 1.1.0), stringr (>= 1.3.1), tibble (>= 3.0.0), tidyselect (>= 1.0.0) NA covr, knitr, paletteer, testthat (>= 2.1.0), RColorBrewer, rmarkdown, rvest, shiny, tidyr, webshot, xml2 NA MIT + file LICENSE NA NA NA NA no 4.0.2
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mitools mitools /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 2.4 NA NA DBI, methods, stats NA RODBC, foreign NA GPL-2 NA NA NA NA no 4.0.2
mixOmics mixOmics /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 6.12.1 NA R (>= 3.5.0), MASS, lattice, ggplot2 igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils NA BiocStyle, knitr, rmarkdown, testthat, rgl NA GPL (>= 2) NA NA NA NA no 4.0.0
mnormt mnormt /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 2.0.1 NA R (>= 4.0.0) tmvnsim (>= 1.0-2) NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
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spotifyr spotifyr /home/konrad/R/x86_64-pc-linux-gnu-library/4.0 2.1.1 NA R (>= 3.3.0) dplyr, purrr, tidyr, httr, lubridate, jsonlite, readr, rvest, stringr, tibble, janitor NA testthat, genius NA MIT + file LICENSE NA NA NA NA no 4.0.2
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BiocCheck BiocCheck /usr/lib/R/site-library 1.24.0 NA R (>= 3.5.0) biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr, tools, optparse, codetools, methods, utils, knitr NA RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1), usethis, BiocStyle codetoolsBioC Artistic-2.0 NA NA NA NA no 4.0.0
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Biocomb Biocomb /usr/lib/R/site-library 0.4 NA R (>= 2.13.0),gtools,Rcpp (>= 0.12.1) rgl, MASS, e1071, randomForest, pROC, ROCR, arules, pamr, class, nnet, rpart, FSelector, RWeka, grDevices, graphics, stats, utils Rcpp NA NA GPL (>= 3) NA NA NA NA yes 4.0.0
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BradleyTerry2 BradleyTerry2 /usr/lib/R/site-library 1.1-2 NA R (>= 2.10) brglm, gtools, lme4 (>= 1.0), qvcalc, stats NA prefmod, testthat gnm GPL (>= 2) NA NA NA NA no 4.0.0
C50 C50 /usr/lib/R/site-library 0.1.3.1 NA R (>= 2.10.0) partykit, Cubist (>= 0.2.3) NA knitr, modeldata NA GPL-3 NA NA NA NA yes 4.0.0
Cairo Cairo /usr/lib/R/site-library 1.5-12.2 NA R (>= 2.4.0) grDevices, graphics NA png FastRWeb GPL-2 NA NA NA NA yes 4.0.2
CircStats CircStats /usr/lib/R/site-library 0.2-6 NA MASS, boot NA NA NA NA GPL-2 NA NA NA NA no 4.0.0
ComplexHeatmap ComplexHeatmap /usr/lib/R/site-library 2.4.2 NA R (>= 3.1.2), methods, grid, graphics, stats, grDevices circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png NA testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext NA MIT + file LICENSE NA NA NA NA no 4.0.0
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DBI DBI /usr/lib/R/site-library 1.1.0 NA methods, R (>= 3.0.0) NA NA blob, covr, hms, knitr, magrittr, rmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat, xml2 NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
DESeq DESeq /usr/lib/R/site-library 1.39.0 NA BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice genefilter, geneplotter, methods, MASS, RColorBrewer NA pasilla (>= 0.2.10), vsn, gplots NA GPL (>= 3) NA NA NA NA yes 4.0.0
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DEoptimR DEoptimR /usr/lib/R/site-library 1.0-8 NA NA stats NA NA robustbase GPL (>= 2) NA NA NA NA no 4.0.0
DMwR DMwR /usr/lib/R/site-library 0.4.1 NA R(>= 2.10), methods, graphics, lattice (>= 0.18-3), grid (>= 2.10.1) xts (>= 0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>= 1.1-0), rpart (>= 3.1-46), class (>= 7.3-1), ROCR (>= 1.0) NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
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DOSE DOSE /usr/lib/R/site-library 3.14.0 NA R (>= 3.4.0) AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, stats, utils NA prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat NA Artistic-2.0 NA NA NA NA no 4.0.0
DT DT /usr/lib/R/site-library 0.14 NA NA htmltools (>= 0.3.6), htmlwidgets (>= 1.3), jsonlite (>= 0.9.16), magrittr, crosstalk, promises NA knitr (>= 1.8), rmarkdown, shiny (>= 1.2.0), testit NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
DelayedArray DelayedArray /usr/lib/R/site-library 0.14.1 NA R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.25.15), IRanges (>= 2.17.3) stats, Matrix S4Vectors BiocParallel, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit NA Artistic-2.0 NA NA NA NA yes 4.0.2
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Deriv Deriv /usr/lib/R/site-library 4.0 NA NA methods NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
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FactoMineR FactoMineR /usr/lib/R/site-library 2.3 NA R (>= 3.5.0) car,cluster,ellipse,flashClust,graphics,grDevices,lattice,leaps,MASS,scatterplot3d,stats,utils,ggplot2,ggrepel NA missMDA,knitr,Factoshiny NA GPL (>= 2) NA NA NA NA no 4.0.0
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GA GA /usr/lib/R/site-library 3.2 NA R (>= 3.4), methods, foreach, iterators stats, graphics, grDevices, utils, cli, crayon, Rcpp Rcpp, RcppArmadillo parallel, doParallel, doRNG (>= 1.6), knitr (>= 1.8) NA GPL (>= 2) NA NA NA NA yes 4.0.0
GDCRNATools GDCRNATools /usr/lib/R/site-library 1.8.0 NA R (>= 3.5.0) shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel NA knitr, testthat NA Artistic-2.0 NA NA NA NA no 4.0.0
GGally GGally /usr/lib/R/site-library 2.0.0 NA R (>= 3.1), ggplot2 (>= 3.3.0) grDevices, grid, gtable (>= 0.2.0), plyr (>= 1.8.3), progress, RColorBrewer, reshape (>= 0.8.5), scales (>= 1.1.0), utils, rlang, lifecycle NA broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), ggforce, Hmisc, igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, sna (>= 2.3-2), survival, rmarkdown, roxygen2, testthat, crosstalk, knitr, spelling NA GPL (>= 2.0) NA NA NA NA no 4.0.0
GO.db GO.db /usr/lib/R/site-library 3.11.4 NA R (>= 2.7.0), methods, AnnotationDbi (>= 1.49.2) methods, AnnotationDbi NA DBI NA Artistic-2.0 NA NA NA NA no 4.0.0
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GetoptLong GetoptLong /usr/lib/R/site-library 1.0.2 NA R (>= 3.3.0) rjson, GlobalOptions (>= 0.1.0), methods, crayon NA testthat (>= 1.0.0), knitr, markdown NA MIT + file LICENSE NA NA NA NA no 4.0.2
GlobalOptions GlobalOptions /usr/lib/R/site-library 0.1.2 NA R (>= 3.3.0), methods utils NA testthat (>= 1.0.0), knitr, markdown, GetoptLong NA MIT + file LICENSE NA NA NA NA no 4.0.0
Hmisc Hmisc /usr/lib/R/site-library 4.4-0 NA lattice, survival (>= 3.1-6), Formula, ggplot2 (>= 2.2) methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, htmltools, base64enc NA chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= 4.5.6), rlang NA GPL (>= 2) NA NA NA NA yes 4.0.0
IRanges IRanges /usr/lib/R/site-library 2.22.2 NA R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.25.14) stats4 S4Vectors XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle NA Artistic-2.0 NA NA NA NA yes 4.0.0
ISwR ISwR /usr/lib/R/site-library 2.0-8 NA R (>= 2.6.0) NA NA survival,MASS NA GPL (>= 2) NA NA NA NA no 4.0.0
KEGGREST KEGGREST /usr/lib/R/site-library 1.28.0 NA NA methods, httr, png, Biostrings NA RUnit, BiocGenerics, knitr NA Artistic-2.0 NA NA NA NA no 4.0.0
KEGGgraph KEGGgraph /usr/lib/R/site-library 1.48.0 NA R (>= 2.10.0) methods, XML (>= 2.3-0), graph, utils, RCurl NA Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA NA GPL (>= 2) NA NA NA NA no 4.0.0
KMsurv KMsurv /usr/lib/R/site-library 0.1-5 NA NA NA NA NA NA GPL (>= 3) NA NA NA NA NA 4.0.0
KernSmooth KernSmooth /usr/lib/R/site-library 2.23-17 recommended R (>= 2.5.0), stats NA NA MASS NA Unlimited NA NA NA NA yes 4.0.0
Lahman Lahman /usr/lib/R/site-library 8.0-0 NA R (>= 3.5.0) dplyr NA lattice, ggplot2, googleVis, data.table, vcd, reshape2, tidyr, knitr, rmarkdown, car NA GPL NA NA NA NA no 4.0.0
LambertW LambertW /usr/lib/R/site-library 0.6.5 NA MASS, ggplot2, lamW (>= 1.3.0), stats, graphics, grDevices, RColorBrewer, reshape2, Rcpp (>= 1.0.4), methods Rcpp, lamW boot, Rsolnp, nortest, numDeriv, testthat, data.table, moments, knitr, vars, NA GPL (>= 2) NA NA NA NA yes 4.0.0
LiblineaR LiblineaR /usr/lib/R/site-library 2.10-8 NA NA NA NA SparseM NA GPL-2 NA NA NA NA yes 4.0.0
LogicReg LogicReg /usr/lib/R/site-library 1.6.2 NA R (>= 2.10), survival stats, graphics, utils, grDevices NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
MASS MASS /usr/lib/R/site-library 7.3-51.6 recommended R (>= 3.1.0), grDevices, graphics, stats, utils methods NA lattice, nlme, nnet, survival NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
MLmetrics MLmetrics /usr/lib/R/site-library 1.1.1 NA R (>= 2.10) stats, utils, ROCR NA e1071 NA GPL-2 NA NA NA NA no 4.0.0
MatchIt MatchIt /usr/lib/R/site-library 3.0.2 NA R (>= 2.6) MASS, Matching NA cem, nnet, optmatch, rpart, mgcv, WhatIf, R.rsp, testthat, rgenoud NA GPL (>= 2) NA NA NA NA no 4.0.0
Matching Matching /usr/lib/R/site-library 4.9-7 NA R (>= 2.6.0), MASS (>= 7.2-1), graphics, grDevices, stats NA NA parallel, rgenoud (>= 2.12), rbounds NA GPL-3 NA NA NA NA yes 4.0.0
Matrix Matrix /usr/lib/R/site-library 1.2-18 recommended R (>= 3.2.0) methods, graphics, grid, stats, utils, lattice NA expm, MASS MatrixModels, graph, SparseM, sfsmisc GPL (>= 2) | file LICENCE NA NA NA NA yes 4.0.0
MatrixModels MatrixModels /usr/lib/R/site-library 0.4-1 NA R (>= 3.0.1) stats, methods, Matrix (>= 1.1-5) NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
ModelMetrics ModelMetrics /usr/lib/R/site-library 1.2.2.2 NA R (>= 3.2.2) Rcpp, data.table Rcpp testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
My.stepwise My.stepwise /usr/lib/R/site-library 0.1.0 NA R (>= 3.3.3) car, lmtest, survival, stats NA NA NA GPL (>= 3) NA NA NA NA no 4.0.0
NLP NLP /usr/lib/R/site-library 0.2-0 NA R (>= 3.2.0) utils NA NA udpipe, spacyr, cleanNLP GPL-3 NA NA NA NA no 4.0.0
PASWR PASWR /usr/lib/R/site-library 1.1 NA e1071, MASS, lattice NA NA NA NA GPL (>= 2) NA NA NA NA NA 4.0.0
PairedData PairedData /usr/lib/R/site-library 1.1.1 NA methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2 NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
ParamHelpers ParamHelpers /usr/lib/R/site-library 1.14 NA NA backports, BBmisc (>= 1.10), checkmate (>= 1.8.2), fastmatch, methods NA akima, covr, eaf, emoa, GGally, ggplot2, grid, gridExtra, irace (>= 2.1), lhs, plyr, reshape2, testthat NA BSD_2_clause + file LICENSE NA NA NA NA yes 4.0.0
R.cache R.cache /usr/lib/R/site-library 0.14.0 NA R (>= 2.14.0) utils, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.8.0), digest (>= 0.6.13) NA NA NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
R.methodsS3 R.methodsS3 /usr/lib/R/site-library 1.8.0 NA R (>= 2.13.0) utils NA codetools NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
R.oo R.oo /usr/lib/R/site-library 1.23.0 NA R (>= 2.13.0), R.methodsS3 (>= 1.7.1) methods, utils NA tools NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
R.utils R.utils /usr/lib/R/site-library 2.9.2 NA R (>= 2.14.0), R.oo (>= 1.23.0) methods, utils, tools, R.methodsS3 (>= 1.7.1) NA digest (>= 0.6.10) NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
R6 R6 /usr/lib/R/site-library 2.4.1 NA R (>= 3.0) NA NA knitr, microbenchmark, pryr, testthat, ggplot2, scales NA MIT + file LICENSE NA NA NA NA no 4.0.0
RANN RANN /usr/lib/R/site-library 2.6.1 NA NA NA NA testthat NA GPL (>= 3) NA NA NA NA yes 4.0.0
RBGL RBGL /usr/lib/R/site-library 1.64.0 NA graph, methods methods BH Rgraphviz, XML, RUnit, BiocGenerics NA Artistic-2.0 NA NA NA NA yes 4.0.0
RColorBrewer RColorBrewer /usr/lib/R/site-library 1.1-2 NA R (>= 2.0.0) NA NA NA NA Apache License 2.0 NA NA NA NA no 4.0.0
RCurl RCurl /usr/lib/R/site-library 1.98-1.2 NA R (>= 3.4.0), methods bitops NA XML NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
RISmed RISmed /usr/lib/R/site-library 2.1.7 NA R (>= 2.8.0), methods NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
RMySQL RMySQL /usr/lib/R/site-library 0.10.20 NA R (>= 2.8.0), DBI (>= 0.4) methods NA RMariaDB, testthat, curl NA GPL-2 NA NA NA NA yes 4.0.0
RNifti RNifti /usr/lib/R/site-library 1.1.0 NA NA Rcpp (>= 0.11.0) Rcpp testthat (>= 0.11.0), covr, reportr, shades oro.nifti, tractor.base GPL-2 NA NA NA NA yes 4.0.0
ROCR ROCR /usr/lib/R/site-library 1.0-11 NA R (>= 3.6) methods, graphics, grDevices, gplots, stats NA testthat, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 4.0.0
RODBC RODBC /usr/lib/R/site-library 1.3-17 NA R (>= 4.0.0) stats NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
ROSE ROSE /usr/lib/R/site-library 0.0-3 NA NA NA NA MASS, nnet, rpart, tree NA GPL-2 NA NA NA NA no 4.0.0
RPostgreSQL RPostgreSQL /usr/lib/R/site-library 0.6-2 NA R (>= 2.9.0), methods, DBI (>= 0.3) NA NA NA NA GPL-2 | file LICENSE NA NA NA NA yes 4.0.0
RRF RRF /usr/lib/R/site-library 1.9.1 NA R (>= 2.5.0), stats NA NA RColorBrewer, MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
RSNNS RSNNS /usr/lib/R/site-library 0.4-12 NA R (>= 2.10.0), methods, Rcpp (>= 0.8.5) NA Rcpp scatterplot3d,NeuralNetTools NA LGPL (>= 2) | file LICENSE NA NA NA NA yes 4.0.0
RSQLite RSQLite /usr/lib/R/site-library 2.2.0 NA R (>= 3.1.0) bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, pkgconfig, Rcpp (>= 0.12.7) BH, plogr (>= 0.2.0), Rcpp DBItest (>= 1.7.0), knitr, rmarkdown, testthat NA LGPL (>= 2.1) NA NA NA NA yes 4.0.0
RSpectra RSpectra /usr/lib/R/site-library 0.16-0 NA R (>= 3.0.2) Matrix (>= 1.1-0), Rcpp (>= 0.11.5) Rcpp, RcppEigen (>= 0.3.3.3.0) knitr, rmarkdown, prettydoc NA MPL (>= 2) NA NA NA NA yes 4.0.0
RUnit RUnit /usr/lib/R/site-library 0.4.32 NA R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0), graphics (>= 2.5.0) NA NA XML (>= 3.1.0) NA GPL-2 NA NA NA NA no 4.0.0
RViennaCL RViennaCL /usr/lib/R/site-library 1.7.1.8 NA NA NA NA gpuR NA GPL-3 NA NA NA NA no 4.0.0
RWeka RWeka /usr/lib/R/site-library 0.4-42 NA R (>= 2.6.0) RWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats, utils, grid NA partykit (>= 0.8.0), mlbench, e1071 NA GPL-2 NA NA NA NA no 4.0.0
RWekajars RWekajars /usr/lib/R/site-library 3.9.3-2 NA NA rJava (>= 0.6-3) NA NA NA GPL-2 NA NA NA NA no 4.0.0
Rcpp Rcpp /usr/lib/R/site-library 1.0.5 NA NA methods, utils NA tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) NA GPL (>= 2) NA NA NA NA yes 4.0.2
RcppAnnoy RcppAnnoy /usr/lib/R/site-library 0.0.16 NA R (>= 3.1) methods, Rcpp (>= 0.11.3) Rcpp tinytest NA GPL (>= 2) NA NA NA NA yes 4.0.0
RcppArmadillo RcppArmadillo /usr/lib/R/site-library 0.9.900.2.0 NA R (>= 3.3.0) Rcpp (>= 0.11.0), stats, utils, methods Rcpp tinytest, Matrix, pkgKitten, reticulate, slam NA GPL (>= 2) NA NA NA NA yes 4.0.2
RcppCNPy RcppCNPy /usr/lib/R/site-library 0.2.10 NA R (>= 3.1.0) methods, Rcpp Rcpp knitr, rmarkdown, pinp, reticulate NA GPL (>= 2) NA NA NA NA yes 4.0.0
RcppEigen RcppEigen /usr/lib/R/site-library 0.3.3.7.0 NA R (>= 2.15.1) Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils Rcpp inline, tinytest, pkgKitten, microbenchmark NA GPL (>= 2) | file LICENSE NA NA NA NA yes 4.0.0
RcppHNSW RcppHNSW /usr/lib/R/site-library 0.2.0 NA NA methods, Rcpp (>= 0.11.3) Rcpp testthat, covr NA GPL-3 NA NA NA NA yes 4.0.0
RcppNumerical RcppNumerical /usr/lib/R/site-library 0.4-0 NA NA Rcpp Rcpp, RcppEigen knitr, rmarkdown, prettydoc, mvtnorm, RcppEigen NA GPL (>= 2) NA NA NA NA yes 4.0.0
RcppParallel RcppParallel /usr/lib/R/site-library 5.0.2 NA R (>= 3.0.2) NA NA Rcpp, RUnit, knitr, rmarkdown NA GPL-2 NA NA NA NA yes 4.0.0
RcppRoll RcppRoll /usr/lib/R/site-library 0.3.0 NA R (>= 2.15.1) Rcpp Rcpp zoo, testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
RefManageR RefManageR /usr/lib/R/site-library 1.2.12 NA R (>= 3.0) xml2, jsonlite, utils, plyr, tools, httr, bibtex (>= 0.4.1), lubridate (>= 1.5.0), stringr, methods NA knitr, testthat, NA GPL-2 | GPL-3 | BSD_3_clause + file LICENSE NA NA NA NA no 4.0.0
Rgraphviz Rgraphviz /usr/lib/R/site-library 2.32.0 NA R (>= 2.6.0), methods, utils, graph, grid stats4, graphics, grDevices NA RUnit, BiocGenerics, XML NA EPL NA NA NA NA yes 4.0.0
Rhtslib Rhtslib /usr/lib/R/site-library 1.20.0 NA NA zlibbioc zlibbioc BiocStyle, knitr NA LGPL (>= 2) NA NA NA NA yes 4.0.0
Rook Rook /usr/lib/R/site-library 1.1-1 NA R (>= 2.13.0) utils, tools, methods, brew NA NA NA GPL-2 NA NA NA NA yes 4.0.0
Rsamtools Rsamtools /usr/lib/R/site-library 2.4.0 NA methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle NA Artistic-2.0 | file LICENSE NA NA NA NA yes 4.0.0
S4Vectors S4Vectors /usr/lib/R/site-library 0.26.1 NA R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>= 0.31.1) NA NA IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle NA Artistic-2.0 NA NA NA NA yes 4.0.0
SQUAREM SQUAREM /usr/lib/R/site-library 2020.3 NA R (>= 3.0) NA NA setRNG NA GPL (>= 2) NA NA NA NA no 4.0.0
ShortRead ShortRead /usr/lib/R/site-library 1.46.0 NA BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, S4Vectors, IRanges, XVector, Biostrings BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi NA Artistic-2.0 NA NA NA NA yes 4.0.0
SnowballC SnowballC /usr/lib/R/site-library 0.7.0 NA NA NA NA NA NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
SparseM SparseM /usr/lib/R/site-library 1.78 NA R (>= 2.15), methods graphics, stats, utils NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
SummarizedExperiment SummarizedExperiment /usr/lib/R/site-library 1.18.2 NA R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.13.1) NA annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat NA Artistic-2.0 NA NA NA NA no 4.0.2
SuppDists SuppDists /usr/lib/R/site-library 1.1-9.5 NA R (>= 3.3.0) NA NA RcppZiggurat NA GPL (>= 2) NA NA NA NA yes 4.0.0
TCGAbiolinks TCGAbiolinks /usr/lib/R/site-library 2.16.3 NA R (>= 3.5) downloader (>= 0.4), grDevices, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) NA jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, TCGAbiolinksGUI.data, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid NA GPL (>= 3) NA NA NA NA no 4.0.2
TH.data TH.data /usr/lib/R/site-library 1.0-10 NA R (>= 2.10.0), survival, MASS NA NA dplyr, gdata, plyr NA GPL-3 NA NA NA NA no 4.0.0
TSP TSP /usr/lib/R/site-library 1.1-10 NA R (>= 3.5.0) graphics, foreach, utils, stats, grDevices NA sp, maps, maptools, testthat NA GPL-3 NA NA NA NA yes 4.0.0
TTR TTR /usr/lib/R/site-library 0.23-6 NA NA xts (>= 0.10-0), zoo, curl xts RUnit quantmod GPL (>= 2) NA NA NA NA yes 4.0.0
TeachingDemos TeachingDemos /usr/lib/R/site-library 2.12 NA R (>= 2.10) NA NA tkrplot, lattice, MASS, rgl, tcltk, tcltk2, png, ggplot2, logspline, maptools, R2wd, manipulate NA Artistic-2.0 NA NA NA NA no 4.0.0
UpSetR UpSetR /usr/lib/R/site-library 1.4.0 NA R (>= 3.0) ggplot2, gridExtra, plyr, utils, stats, methods, grDevices, scales NA knitr NA MIT + file LICENSE NA NA NA NA no 4.0.0
VIM VIM /usr/lib/R/site-library 6.0.0 NA R (>= 3.5.0),colorspace,grid car, grDevices, magrittr, robustbase, stats, sp, vcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger, data.table(>= 1.9.4) Rcpp dplyr, testthat (>= 2.1.0), knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 4.0.0
VennDiagram VennDiagram /usr/lib/R/site-library 1.6.20 NA R (>= 2.14.1), grid (>= 2.14.1), futile.logger NA NA testthat NA GPL-2 NA NA NA NA no 4.0.0
XLConnect XLConnect /usr/lib/R/site-library 1.0.1 NA R (>= 2.10.0) methods, rJava NA RUnit, lattice, ggplot2 (>= 0.9.3), zoo NA GPL-3 NA NA NA NA no 4.0.0
XML XML /usr/lib/R/site-library 3.99-0.4 NA R (>= 4.0.0), methods, utils NA NA bitops, RCurl NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
XVector XVector /usr/lib/R/site-library 0.28.0 NA R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6) methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges S4Vectors, IRanges Biostrings, drosophila2probe, RUnit NA Artistic-2.0 NA NA NA NA yes 4.0.0
abind abind /usr/lib/R/site-library 1.4-5 NA R (>= 1.5.0) methods, utils NA NA NA LGPL (>= 2) NA NA NA NA no 4.0.0
acepack acepack /usr/lib/R/site-library 1.4.1 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
ada ada /usr/lib/R/site-library 2.0-5 NA R(>= 2.10),rpart NA NA NA NA GPL NA NA NA NA no 4.0.0
additivityTests additivityTests /usr/lib/R/site-library 1.1-4 NA NA NA NA knitr NA GPL-3 NA NA NA NA no 4.0.0
ade4 ade4 /usr/lib/R/site-library 1.7-15 NA R (>= 2.10) graphics, grDevices, methods, stats, utils, MASS, pixmap, sp NA ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir, lattice, spdep, splancs, waveslim NA GPL (>= 2) NA NA NA NA yes 4.0.0
airports airports /usr/lib/R/site-library 0.1.0 NA R (>= 2.10) NA NA testthat NA GPL-3 NA NA NA NA no 4.0.0
amap amap /usr/lib/R/site-library 0.8-18 NA R (>= 3.6.0) NA NA Biobase NA GPL NA NA NA NA yes 4.0.0
annotate annotate /usr/lib/R/site-library 1.66.0 NA R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl NA hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, NA Artistic-2.0 NA NA NA NA no 4.0.0
ape ape /usr/lib/R/site-library 5.4 NA R (>= 3.2.0) nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0) Rcpp gee, expm, igraph NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
aroma.light aroma.light /usr/lib/R/site-library 3.18.0 NA R (>= 2.15.2) stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) NA princurve (>= 2.1.4) NA GPL (>= 2) NA NA NA NA no 4.0.0
arules arules /usr/lib/R/site-library 1.6-6 NA R (>= 3.4.0), Matrix (>= 1.2-0) stats, methods, graphics, utils NA pmml, XML, arulesViz, testthat NA GPL-3 NA NA NA NA yes 4.0.0
arulesViz arulesViz /usr/lib/R/site-library 1.3-3 NA arules (>= 1.4.1), grid scatterplot3d, vcd, seriation, igraph (>= 1.0.0), graphics, methods, utils, grDevices, stats, colorspace, DT, plotly, visNetwork NA graph, Rgraphviz, iplots, shiny, shinythemes, htmlwidgets NA GPL-3 NA NA NA NA no 4.0.0
askpass askpass /usr/lib/R/site-library 1.1 NA NA sys (>= 2.1) NA testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
assertive assertive /usr/lib/R/site-library 0.3-5.1 NA R (>= 3.0.0) assertive.base (>= 0.0-4), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), assertive.numbers, assertive.strings, assertive.datetimes, assertive.files, assertive.sets (>= 0.0-2), assertive.matrices, assertive.models, assertive.data, assertive.data.uk, assertive.data.us, assertive.reflection (>= 0.0-2), assertive.code, knitr NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.2
assertive.base assertive.base /usr/lib/R/site-library 0.0-7 NA R (>= 3.0.0) methods, utils NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.code assertive.code /usr/lib/R/site-library 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.properties, assertive.types, methods NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.data assertive.data /usr/lib/R/site-library 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.data.uk assertive.data.uk /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.data.us assertive.data.us /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat, devtools NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.datetimes assertive.datetimes /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.types NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.files assertive.files /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.numbers NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.matrices assertive.matrices /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2) NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.models assertive.models /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), stats NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.numbers assertive.numbers /usr/lib/R/site-library 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2) NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.properties assertive.properties /usr/lib/R/site-library 0.0-4 NA R (>= 3.0.0) assertive.base (>= 0.0-7), methods NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.reflection assertive.reflection /usr/lib/R/site-library 0.0-4.1 NA R (>= 3.0.0) assertive.base (>= 0.0-7), utils NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.2
assertive.sets assertive.sets /usr/lib/R/site-library 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-7) NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.strings assertive.strings /usr/lib/R/site-library 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.types, stringi NA testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
assertive.types assertive.types /usr/lib/R/site-library 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-7), assertive.properties, codetools, methods, stats NA testthat, data.table, dplyr, xml2 NA GPL (>= 3) NA NA NA NA no 4.0.0
assertthat assertthat /usr/lib/R/site-library 0.2.1 NA NA tools NA testthat, covr NA GPL-3 NA NA NA NA no 4.0.0
backports backports /usr/lib/R/site-library 1.1.8 NA R (>= 3.0.0) utils NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
bartMachine bartMachine /usr/lib/R/site-library 1.2.5 NA R (>= 2.14.0), rJava (>= 0.9-8), bartMachineJARs (>= 1.0), randomForest, missForest graphics, grDevices, stats NA NA NA GPL-3 NA NA NA NA no 4.0.2
bartMachineJARs bartMachineJARs /usr/lib/R/site-library 1.1 NA R (>= 2.14.0), rJava (>= 0.9-8) NA NA NA NA GPL-3 NA NA NA NA no 4.0.0
base64enc base64enc /usr/lib/R/site-library 0.1-3 NA R (>= 2.9.0) NA NA NA png GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
bbmle bbmle /usr/lib/R/site-library 1.0.23.1 NA R (>= 3.0.0), stats4 stats, numDeriv, lattice, MASS, methods, bdsmatrix, Matrix, mvtnorm NA emdbook, rms, ggplot2, RUnit, MuMIn, AICcmodavg, Hmisc, optimx (>= 2013.8.6), knitr, testthat NA GPL NA NA NA NA no 4.0.0
bdsmatrix bdsmatrix /usr/lib/R/site-library 1.3-4 NA methods, R (>= 2.0.0) NA NA NA NA LGPL-2 NA NA NA NA yes 4.0.0
beeswarm beeswarm /usr/lib/R/site-library 0.2.3 NA NA stats, graphics, grDevices, utils NA NA NA Artistic-2.0 NA NA NA NA no 4.0.0
bench bench /usr/lib/R/site-library 1.1.1 NA R (>= 3.1) glue, methods, pillar, profmem, rlang (>= 0.2.0), stats, tibble, utils NA covr, dplyr, forcats, ggbeeswarm, ggplot2, ggridges, mockery, parallel, scales, testthat, tidyr (>= 0.8.1), vctrs, withr NA GPL-3 NA NA NA NA yes 4.0.0
bestNormalize bestNormalize /usr/lib/R/site-library 1.6.1 NA R (>= 3.1.0) LambertW (>= 0.6.5), nortest, dplyr, doParallel, foreach, doRNG, recipes, tibble, methods NA knitr, rmarkdown, MASS, testthat, mgcv, parallel NA GPL-3 NA NA NA NA no 4.0.0
bibtex bibtex /usr/lib/R/site-library 0.4.2.2 NA R (>= 3.0.2) stringr, utils NA testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
biclust biclust /usr/lib/R/site-library 2.0.2 NA R (>= 2.10), MASS, grid, colorspace, lattice methods, flexclust, additivityTests, tidyr, ggplot2 NA isa2 NA GPL-3 NA NA NA NA yes 4.0.0
biocViews biocViews /usr/lib/R/site-library 1.56.2 NA R (>= 3.6.0) Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager NA BiocGenerics, knitr, commonmark NA Artistic-2.0 NA NA NA NA no 4.0.2
biomaRt biomaRt /usr/lib/R/site-library 2.44.1 NA methods utils, XML, AnnotationDbi, progress, stringr, httr, openssl, BiocFileCache, rappdirs NA annotate, BiocStyle, knitr, rmarkdown, testthat NA Artistic-2.0 NA NA NA NA no 4.0.2
bit bit /usr/lib/R/site-library 1.1-15.2 NA R (>= 2.9.2) NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
bit64 bit64 /usr/lib/R/site-library 0.9-7.1 NA R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats NA NA NA NA GPL-2 NA NA NA NA yes 4.0.2
bitops bitops /usr/lib/R/site-library 1.0-6 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
blob blob /usr/lib/R/site-library 1.2.1 NA NA methods, rlang, vctrs (>= 0.2.1) NA covr, crayon, pillar (>= 1.2.1), testthat NA GPL-3 NA NA NA NA no 4.0.0
bmp bmp /usr/lib/R/site-library 0.3 NA NA NA NA pixmap, testthat NA GPL (>= 2) NA NA NA NA no 4.0.0
bookdown bookdown /usr/lib/R/site-library 0.20 NA NA htmltools (>= 0.3.6), knitr (>= 1.22), rmarkdown (>= 2.3), xfun (>= 0.6), tinytex (>= 0.12) NA htmlwidgets, rstudioapi, miniUI, rsconnect (>= 0.4.3), servr (>= 0.13), shiny, testit (>= 0.9), tufte, webshot NA GPL-3 NA NA NA NA no 4.0.0
boot boot /usr/lib/R/site-library 1.3-25 recommended R (>= 3.0.0), graphics, stats NA NA MASS, survival NA Unlimited NA NA NA NA no 4.0.0
bootstrap bootstrap /usr/lib/R/site-library 2019.6 NA stats, R (>= 2.10.0) NA NA NA NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
bounceR bounceR /usr/lib/R/site-library 0.1 NA R (>= 3.4.3) purrr, furrr, parallel, mboost, strucchange, np, reshape2, ggplot2, mRMRe, dplyr, future NA NA NA MIT + file LICENSE NA NA NA NA no 4.0.0
brew brew /usr/lib/R/site-library 1.0-6 NA NA NA NA NA NA GPL-2 NA NA NA NA NA 4.0.0
brglm brglm /usr/lib/R/site-library 0.6.2 NA R (>= 2.6.0), profileModel NA NA MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
broom broom /usr/lib/R/site-library 0.7.0 NA R (>= 3.1) backports, dplyr, ellipsis, generics (>= 0.0.2), glue, methods, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr NA AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, btergm, car, caret, cluster, coda, covr, drc, e1071, emmeans, epiR, ergm, fixest (>= 0.3.1), gam (>= 1.15), gamlss, gamlss.data, gamlss.dist, gee, geepack, ggplot2, glmnet, glmnetUtils, gmm, Hmisc, irlba, joineRML, Kendall, knitr, ks, Lahman, lavaan, leaps, lfe, lm.beta, lme4, lmodel2, lmtest, lsmeans, maps, maptools, MASS, Matrix, mclogit, mclust, mediation, metafor, mfx, mgcv, modeldata, modeltests, muhaz, multcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, poLCA, psych, quantreg, rgeos, rmarkdown, robust, robustbase, rsample, sandwich, sp, spdep, spatialreg, speedglm, spelling, statnet.common, survey, survival, systemfit, testthat (>= 2.1.0), tseries, zoo NA MIT + file LICENSE NA NA NA NA no 4.0.2
ca ca /usr/lib/R/site-library 0.71.1 NA R (>= 3.0.0) NA NA rgl (>= 0.64-10), vcd NA GPL NA NA NA NA no 4.0.0
caTools caTools /usr/lib/R/site-library 1.18.0 NA R (>= 3.6.0) bitops NA MASS, rpart NA GPL-3 NA NA NA NA yes 4.0.0
calibrate calibrate /usr/lib/R/site-library 1.7.7 NA R (>= 3.5.0), MASS NA NA NA NA GPL-2 NA NA NA NA no 4.0.0
callr callr /usr/lib/R/site-library 3.4.3 NA NA processx (>= 3.4.0), R6, utils NA cliapp, covr, crayon, fansi, pingr, ps, rprojroot, spelling, testthat, tibble, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
car car /usr/lib/R/site-library 3.0-8 NA R (>= 3.5.0), carData (>= 3.0-0) abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg, grDevices, utils, stats, graphics, maptools, rio, lme4, nlme NA alr4, boot, coxme, knitr, leaps, lmtest, Matrix, MatrixModels, rgl (>= 0.93.960), sandwich, SparseM, survival, survey NA GPL (>= 2) NA NA NA NA no 4.0.0
carData carData /usr/lib/R/site-library 3.0-4 NA R (>= 3.5.0) NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
caret caret /usr/lib/R/site-library 6.0-86 NA R (>= 3.2.0), lattice (>= 0.20), ggplot2 foreach, methods, plyr, ModelMetrics (>= 1.2.2.2), nlme, reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.10), withr (>= 2.0.0), pROC, NA BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>= 1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv, mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, proxy, randomForest, RANN, spls, subselect, pamr, superpc, Cubist, testthat (>= 0.9.1), rpart, dplyr, covr NA GPL (>= 2) NA NA NA NA yes 4.0.0
caretEnsemble caretEnsemble /usr/lib/R/site-library 2.0.1 NA R (>= 3.2.0) methods, pbapply, ggplot2, digest, plyr, lattice, gridExtra, data.table, caret NA caTools, testthat, lintr, randomForest, glmnet, rpart, kernlab, nnet, e1071, ipred, pROC, knitr, mlbench, MASS, gbm, klaR, rmarkdown NA MIT + file LICENSE NA NA NA NA no 4.0.0
cba cba /usr/lib/R/site-library 0.2-21 NA R (>= 2.10), grid, proxy stats, graphics, grDevices, methods NA gclus, colorspace NA GPL-2 NA NA NA NA yes 4.0.0
cellranger cellranger /usr/lib/R/site-library 1.1.0 NA R (>= 3.0.0) rematch, tibble NA covr, testthat (>= 1.0.0), knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA no 4.0.0
checkmate checkmate /usr/lib/R/site-library 2.0.0 NA R (>= 3.0.0) backports (>= 1.1.0), utils NA R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2, knitr, magrittr, microbenchmark, rmarkdown, testthat (>= 0.11.0), tinytest (>= 1.1.0), tibble NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
cherryblossom cherryblossom /usr/lib/R/site-library 0.1.0 NA R (>= 2.10) NA NA ggplot2, testthat NA GPL-3 NA NA NA NA no 4.0.0
chron chron /usr/lib/R/site-library 2.3-55 NA R (>= 2.12.0) graphics, stats NA scales, ggplot2 zoo GPL-2 NA NA NA NA yes 4.0.0
circlize circlize /usr/lib/R/site-library 0.4.10 NA R (>= 3.0.0), graphics GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats, colorspace, methods, grid NA knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase, png NA MIT + file LICENSE NA NA NA NA no 4.0.0
class class /usr/lib/R/site-library 7.3-17 recommended R (>= 3.0.0), stats, utils MASS NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
classInt classInt /usr/lib/R/site-library 0.4-3 NA R (>= 2.2) grDevices, stats, graphics, e1071, class, KernSmooth NA spData (>= 0.2.6.2), units, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 4.0.0
cli cli /usr/lib/R/site-library 2.0.2 NA R (>= 2.10) assertthat, crayon (>= 1.3.4), glue, methods, utils, fansi NA callr, covr, htmlwidgets, knitr, mockery, rmarkdown, rstudioapi, prettycode (>= 1.1.0), testthat, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
clipr clipr /usr/lib/R/site-library 0.7.0 NA NA utils NA covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>= 2.0.0) NA GPL-3 NA NA NA NA no 4.0.0
clisymbols clisymbols /usr/lib/R/site-library 1.2.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
clue clue /usr/lib/R/site-library 0.3-57 NA R (>= 3.2.0) stats, cluster, graphics, methods NA e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust, movMF, modeltools GPL-2 NA NA NA NA yes 4.0.0
cluster cluster /usr/lib/R/site-library 2.1.0 recommended R (>= 3.3.0) graphics, grDevices, stats, utils NA MASS, Matrix NA GPL (>= 2) NA NA NA NA yes 4.0.0
clusterProfiler clusterProfiler /usr/lib/R/site-library 3.16.0 NA R (>= 3.4.0) AnnotationDbi, downloader, DOSE (>= 3.13.1), dplyr, enrichplot (>= 1.7.1), GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rlang, rvcheck, stats, tidyr, utils NA AnnotationHub, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat NA Artistic-2.0 NA NA NA NA no 4.0.0
clv clv /usr/lib/R/site-library 0.3-2.2 NA cluster, class NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
cmprsk cmprsk /usr/lib/R/site-library 2.2-10 NA R (>= 3.0.0), survival NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
coda coda /usr/lib/R/site-library 0.19-3 NA R (>= 2.14.0) lattice NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
codetools codetools /usr/lib/R/site-library 0.2-16 recommended R (>= 2.1) NA NA NA NA GPL NA NA NA NA no 4.0.0
coin coin /usr/lib/R/site-library 1.3-1 NA R (>= 3.4.0), survival methods, parallel, stats, stats4, utils, libcoin (>= 1.0-0), matrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>= 1.0-5), multcomp libcoin (>= 1.0-0) xtable, e1071, vcd, TH.data (>= 1.0-7) NA GPL-2 NA NA NA NA yes 4.0.0
colorspace colorspace /usr/lib/R/site-library 1.4-1 NA R (>= 3.0.0), methods graphics, grDevices, stats NA datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd, tcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg, knitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis, wesanderson NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
combinat combinat /usr/lib/R/site-library 0.0-8 NA NA NA NA NA NA GPL-2 NA NA NA NA NA 4.0.0
commonmark commonmark /usr/lib/R/site-library 1.7 NA NA NA NA curl, testthat, xml2 NA BSD_2_clause + file LICENSE NA NA NA NA yes 4.0.0
compare compare /usr/lib/R/site-library 0.2-6 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
config config /usr/lib/R/site-library 0.3 NA NA yaml (>= 2.1.13) NA testthat, knitr NA GPL-3 NA NA NA NA no 4.0.0
conquer conquer /usr/lib/R/site-library 1.0.1 NA R (>= 3.6.0) Rcpp (>= 1.0.3), Matrix, matrixStats, stats Rcpp, RcppArmadillo NA NA GPL-3 NA NA NA NA yes 4.0.2
corpcor corpcor /usr/lib/R/site-library 1.6.9 NA R (>= 3.0.2) stats NA NA GPL (>= 3) NA NA NA NA no 4.0.0
corrplot corrplot /usr/lib/R/site-library 0.84 NA NA NA NA knitr, RColorBrewer, testthat NA GPL NA NA NA NA no 4.0.0
covr covr /usr/lib/R/site-library 3.5.0 NA R (>= 3.1.0), methods digest, stats, utils, jsonlite, rex, httr, crayon, withr (>= 1.0.2), yaml NA R6, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat, rlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise, mockery NA GPL-3 NA NA NA NA yes 4.0.0
cowplot cowplot /usr/lib/R/site-library 1.0.0 NA R (>= 3.5.0) ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang, scales, utils NA Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr, lattice, magick, maps, PASWR, rmarkdown, testthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram NA GPL-2 NA NA NA NA no 4.0.0
crayon crayon /usr/lib/R/site-library 1.3.4 NA NA grDevices, methods, utils NA mockery, rstudioapi, testthat, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
crosstalk crosstalk /usr/lib/R/site-library 1.1.0.1 NA NA htmltools (>= 0.3.6), jsonlite, lazyeval, R6 NA shiny, ggplot2, testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA no 4.0.0
crrstep crrstep /usr/lib/R/site-library 2015-2.1 NA cmprsk NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
crul crul /usr/lib/R/site-library 0.9.0 NA NA curl (>= 3.3), R6 (>= 2.2.0), urltools (>= 1.6.0), httpcode (>= 0.2.0), jsonlite, mime NA testthat, fauxpas (>= 0.1.0), webmockr (>= 0.1.0), knitr NA MIT + file LICENSE NA NA NA NA no 4.0.0
cubature cubature /usr/lib/R/site-library 2.0.4.1 NA NA Rcpp Rcpp testthat, knitr, mvtnorm, benchr NA GPL-3 NA NA NA NA yes 4.0.2
curl curl /usr/lib/R/site-library 4.3 NA R (>= 3.0.0) NA NA spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown, magrittr, httpuv (>= 1.4.4), webutils NA MIT + file LICENSE NA NA NA NA yes 4.0.0
cutpointr cutpointr /usr/lib/R/site-library 1.0.32 NA R (>= 3.5.0) gridExtra (>= 2.2.1), foreach (>= 1.4.3), dplyr (>= 0.8.0), tidyr (>= 1.0.0), purrr (>= 0.3.0), tibble (>= 3.0.0), ggplot2 (>= 3.0.0), Rcpp (>= 0.12.12), stats, utils, rlang (>= 0.4.0) Rcpp KernSmooth (>= 2.23-15), fANCOVA (>= 0.5-1), testthat (>= 1.0.2), doRNG (>= 1.6), doParallel (>= 1.0.11), knitr, rmarkdown, mgcv (>= 1.8), crayon (>= 1.3.4), registry (>= 0.5-1), pkgmaker(>= 0.31.1), vctrs (>= 0.2.4) NA GPL-3 NA NA NA NA yes 4.0.0
cyclocomp cyclocomp /usr/lib/R/site-library 1.1.0 NA NA callr, crayon, desc, remotes, withr NA testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
data.table data.table /usr/lib/R/site-library 1.12.8 NA R (>= 3.1.0) methods NA bit64, curl, R.utils, knitr, xts, nanotime, zoo, yaml NA MPL-2.0 | file LICENSE NA NA NA NA yes 4.0.0
dbplyr dbplyr /usr/lib/R/site-library 1.4.4 NA R (>= 3.1) assertthat (>= 0.2.0), DBI (>= 1.0.0), dplyr (>= 0.8.0), glue (>= 1.2.0), lifecycle, magrittr, methods, purrr (>= 0.2.5), R6 (>= 2.2.2), rlang (>= 0.2.0), tibble (>= 1.4.2), tidyselect (>= 0.2.4), blob (>= 1.2.0), utils NA bit64, covr, knitr, Lahman, nycflights13, odbc, RMariaDB (>= 1.0.2), rmarkdown, RPostgres (>= 1.1.3), RSQLite (>= 2.1.0), testthat (>= 2.0.0) NA MIT + file LICENSE NA NA NA NA no 4.0.0
dbscan dbscan /usr/lib/R/site-library 1.1-5 NA NA Rcpp (>= 1.0.0), graphics, stats, methods Rcpp fpc, microbenchmark, testthat, dendextend, igraph, knitr, DMwR NA GPL (>= 2) NA NA NA NA yes 4.0.0
deepnet deepnet /usr/lib/R/site-library 0.2 NA NA NA NA NA NA GPL NA NA NA NA no 4.0.0
dendextend dendextend /usr/lib/R/site-library 1.13.4 NA R (>= 3.0.0) utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis NA knitr, rmarkdown, testthat, seriation, colorspace, ape, microbenchmark, gplots, heatmaply, d3heatmap, dynamicTreeCut, pvclust, corrplot, DendSer, MASS, cluster, fpc, circlize (>= 0.2.5), covr ggdendro, dendroextras, Hmisc, data.table, rpart GPL-2 | GPL-3 NA NA NA NA no 4.0.0
desc desc /usr/lib/R/site-library 1.2.0 NA R (>= 3.1.0) assertthat, utils, R6, crayon, rprojroot NA covr, testthat, whoami, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
descr descr /usr/lib/R/site-library 1.1.4 NA NA xtable, utils, grDevices, graphics, stats NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
desirability desirability /usr/lib/R/site-library 2.1 NA NA stats, graphics, grDevices NA lattice NA GPL-2 NA NA NA NA no 4.0.0
devtools devtools /usr/lib/R/site-library 2.3.0 NA R (>= 3.0.2), usethis (>= 1.6.0) callr (>= 3.4.3), cli (>= 2.0.2), covr (>= 3.5.0), crayon (>= 1.3.4), desc (>= 1.2.0), digest (>= 0.6.25), DT (>= 0.13), ellipsis (>= 0.3.0), glue (>= 1.4.0), git2r (>= 0.26.1), httr (>= 1.4.1), jsonlite (>= 1.6.1), memoise (>= 1.1.0), pkgbuild (>= 1.0.6), pkgload (>= 1.0.2), rcmdcheck (>= 1.3.3), remotes (>= 2.1.1), rlang (>= 0.4.5), roxygen2 (>= 7.1.0), rstudioapi (>= 0.11), rversions (>= 2.0.1), sessioninfo (>= 1.1.1), stats, testthat (>= 2.3.2), tools, utils, withr (>= 2.1.2) NA BiocManager (>= 1.30.10), curl (>= 4.3), foghorn (>= 1.1.5), gmailr (>= 1.0.0), knitr (>= 1.28), lintr (>= 2.0.1), mockery (>= 0.4.2), pingr (>= 2.0.0), MASS, pkgdown (>= 1.5.1), rhub (>= 1.1.1), rmarkdown (>= 2.1), spelling (>= 2.1) NA GPL (>= 2) NA NA NA NA no 4.0.0
diffobj diffobj /usr/lib/R/site-library 0.3.0 NA R (>= 3.1.0) crayon (>= 1.3.2), tools, methods, utils, stats NA knitr, rmarkdown, testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
digest digest /usr/lib/R/site-library 0.6.25 NA R (>= 3.1.0) utils NA tinytest, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 4.0.0
diptest diptest /usr/lib/R/site-library 0.75-7 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
doBy doBy /usr/lib/R/site-library 4.6.7 NA R (>= 3.6.0), methods pbkrtest (>= 0.4-8.1), MASS, Matrix, magrittr, Deriv, tibble, broom, ggplot2, dplyr NA multcomp, geepack, lme4, survival, knitr NA GPL (>= 2) NA NA NA NA no 4.0.2
doParallel doParallel /usr/lib/R/site-library 1.0.15 NA R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0), parallel, utils NA NA caret, mlbench, rpart, RUnit compiler GPL-2 NA NA NA NA no 4.0.0
doRNG doRNG /usr/lib/R/site-library 1.8.2 NA R (>= 3.0.0), foreach, rngtools (>= 1.5) stats, utils, iterators NA doParallel, doMPI, doRedis, rbenchmark, devtools, knitr, bibtex, testthat, pkgmaker (>= 0.31) NA GPL (>= 2) NA NA NA NA no 4.0.0
doSNOW doSNOW /usr/lib/R/site-library 1.0.18 NA R (>= 2.5.0), foreach(>= 1.2.0), iterators(>= 1.0.0), snow(>= 0.3.0), utils NA NA compiler, RUnit, caret, mlbench, rpart, parallel NA GPL-2 NA NA NA NA no 4.0.0
dotCall64 dotCall64 /usr/lib/R/site-library 1.0-0 NA R (>= 3.1) NA NA microbenchmark, OpenMPController, RColorBrewer, roxygen2, spam, testthat, NA GPL (>= 2) NA NA NA NA yes 4.0.0
downloader downloader /usr/lib/R/site-library 0.4 NA NA utils, digest NA testthat NA GPL-2 NA NA NA NA no 4.0.0
dplyr dplyr /usr/lib/R/site-library 1.0.0 NA R (>= 3.2.0) ellipsis, generics, glue (>= 1.3.2), lifecycle (>= 0.2.0), magrittr (>= 1.5), methods, R6, rlang (>= 0.4.6), tibble (>= 2.1.3), tidyselect (>= 1.1.0), utils, vctrs (>= 0.3.0) NA bench, broom, callr, covr, DBI, dbplyr (>= 1.4.3), knitr, Lahman, lobstr, microbenchmark, nycflights13, purrr, rmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat (>= 2.1.0), withr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
dtplyr dtplyr /usr/lib/R/site-library 1.0.1 NA R (>= 3.2) crayon, data.table (>= 1.12.4), dplyr (>= 0.8.1), rlang, tibble, tidyselect NA bench, covr, knitr, rmarkdown, testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 4.0.0
dtw dtw /usr/lib/R/site-library 1.21-3 NA R (>= 2.10.0), proxy graphics, grDevices, stats, utils NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
dynamicTreeCut dynamicTreeCut /usr/lib/R/site-library 1.63-1 NA R (>= 2.3.0), stats NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
e1071 e1071 /usr/lib/R/site-library 1.7-3 NA NA graphics, grDevices, class, stats, methods, utils NA cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable, Matrix, MASS, slam NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
earth earth /usr/lib/R/site-library 5.1.2 NA R (>= 3.4.0), Formula (>= 1.2-3), plotmo (>= 3.5.4), TeachingDemos (>= 2.10) NA NA gam (>= 1.16), mgcv (>= 1.8-26), mda (>= 0.4-10), MASS (>= 7.3-51) NA GPL-3 NA NA NA NA yes 4.0.0
edgeR edgeR /usr/lib/R/site-library 3.30.3 NA R (>= 3.6.0), limma (>= 3.41.5) methods, graphics, stats, utils, locfit, Rcpp Rcpp jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db NA GPL (>=2) NA NA NA NA yes 4.0.2
egg egg /usr/lib/R/site-library 0.4.5 NA gridExtra (>= 2.3), ggplot2 gtable, grid, grDevices, utils NA knitr, png NA GPL-3 NA NA NA NA no 4.0.0
ellipse ellipse /usr/lib/R/site-library 0.4.2 NA R (>= 2.0.0),graphics,stats NA NA MASS NA GPL (>= 2) NA NA NA NA no 4.0.0
ellipsis ellipsis /usr/lib/R/site-library 0.3.1 NA R (>= 3.2) rlang (>= 0.3.0) NA covr, testthat NA GPL-3 NA NA NA NA yes 4.0.0
emdbook emdbook /usr/lib/R/site-library 1.3.12 NA NA MASS, lattice, plyr, coda, bbmle NA R2jags, ellipse, SuppDists, numDeriv, testthat, rgl NA GPL NA NA NA NA no 4.0.0
enc enc /usr/lib/R/site-library 0.2.2 NA R (>= 3.1) methods NA digest, pillar, readr, rlang, testthat, withr NA GPL-3 NA NA NA NA yes 4.0.0
enrichplot enrichplot /usr/lib/R/site-library 1.8.1 NA R (>= 3.4.0) AnnotationDbi, cowplot, DOSE (>= 3.13.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, plyr, purrr, RColorBrewer, reshape2, stats, utils, scatterpie NA clusterProfiler, dplyr, ggupset, knitr, org.Hs.eg.db, prettydoc, tibble, tidyr NA Artistic-2.0 NA NA NA NA no 4.0.0
entropy entropy /usr/lib/R/site-library 1.2.1 NA R (>= 2.15.1) NA NA NA GPL (>= 3) NA NA NA NA no 4.0.0
epiDisplay epiDisplay /usr/lib/R/site-library 3.5.0.1 NA R (>= 2.6.2), foreign, survival, MASS, nnet NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
europepmc europepmc /usr/lib/R/site-library 0.4 NA R (>= 3.00) httr, jsonlite, plyr, dplyr, progress, urltools, purrr, xml2, tibble, tidyr, rlang NA testthat, knitr, rmarkdown, ggplot2 NA GPL-3 NA NA NA NA no 4.0.0
evaluate evaluate /usr/lib/R/site-library 0.14 NA R (>= 3.0.2) methods NA testthat, lattice, ggplot2 NA MIT + file LICENSE NA NA NA NA no 4.0.0
evtree evtree /usr/lib/R/site-library 1.0-8 NA R (>= 3.3.0), partykit NA NA Formula, kernlab, lattice, mlbench, multcomp, party, rpart, xtable NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
exactRankTests exactRankTests /usr/lib/R/site-library 0.8-31 NA R (>= 2.4.0), stats, utils NA NA survival NA GPL (>= 2) NA NA NA NA yes 4.0.0
fBasics fBasics /usr/lib/R/site-library 3042.89.1 NA R (>= 2.15.1), timeDate, timeSeries stats, grDevices, graphics, methods, utils, MASS, spatial, gss, stabledist NA akima, RUnit, tcltk NA GPL (>= 2) NA NA NA NA yes 4.0.0
factoextra factoextra /usr/lib/R/site-library 1.0.7 NA R (>= 3.1.2), ggplot2 (>= 2.2.0) abind, cluster, dendextend, FactoMineR, ggpubr(>= 0.1.5), grid, stats, reshape2, ggrepel, tidyr NA ade4, ca, igraph, MASS, knitr, mclust NA GPL-2 NA NA NA NA no 4.0.0
fansi fansi /usr/lib/R/site-library 0.4.1 NA R (>= 3.1.0) NA NA unitizer, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 4.0.0
farver farver /usr/lib/R/site-library 2.0.3 NA NA NA NA testthat (>= 2.1.0), covr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
fastICA fastICA /usr/lib/R/site-library 1.2-2 NA R (>= 3.0.0) NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
fastmap fastmap /usr/lib/R/site-library 1.0.1 NA NA NA NA testthat (>= 2.1.1) NA MIT + file LICENSE NA NA NA NA yes 4.0.0
fastmatch fastmatch /usr/lib/R/site-library 1.1-0 NA NA NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
fgsea fgsea /usr/lib/R/site-library 1.14.0 NA R (>= 3.3) Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils Rcpp, BH testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery NA MIT + file LICENCE NA NA NA NA yes 4.0.0
fields fields /usr/lib/R/site-library 10.3 NA R (>= 3.0), methods, spam, maps NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
flashClust flashClust /usr/lib/R/site-library 1.01-2 NA R (>= 2.3.0) NA NA NA NA GPL (>= 2) NA NA NA NA NA 4.0.0
flexclust flexclust /usr/lib/R/site-library 1.4-0 NA R (>= 2.14.0), graphics, grid, lattice, modeltools methods, parallel, stats, stats4, class NA ellipse, clue, cluster, seriation, skmeans NA GPL-2 NA NA NA NA yes 4.0.0
flexmix flexmix /usr/lib/R/site-library 2.3-15 NA R (>= 2.15.0), lattice graphics, grid, grDevices, methods, modeltools (>= 0.2-16), nnet, stats, stats4, utils NA actuar, codetools, diptest, Ecdat, ellipse, gclus, glmnet, lme4 (>= 1.1), MASS, mgcv (>= 1.8-0), mlbench, multcomp, mvtnorm, SuppDists, survival NA GPL (>= 2) NA NA NA NA no 4.0.0
foghorn foghorn /usr/lib/R/site-library 1.2.1 NA R (>= 3.1.0) clisymbols (>= 1.0.0), crayon (>= 1.3.2), curl (>= 2.2), httr (>= 1.2.1), jsonlite (>= 1.5), rlang (>= 0.4.3), rvest (>= 0.3.2), tibble (>= 1.2), xml2 (>= 1.0.0) NA covr, dplyr, knitr, progress, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
fontBitstreamVera fontBitstreamVera /usr/lib/R/site-library 0.1.1 NA R (>= 3.0.0) NA NA NA NA file LICENCE yes NA NA NA no 4.0.0
fontLiberation fontLiberation /usr/lib/R/site-library 0.1.0 NA R (>= 3.0) NA NA NA NA file LICENSE yes NA NA NA no 4.0.0
fontquiver fontquiver /usr/lib/R/site-library 0.2.1 NA R (>= 3.0.0) fontBitstreamVera (>= 0.1.0), fontLiberation (>= 0.1.0) NA testthat, htmltools NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
forcats forcats /usr/lib/R/site-library 0.5.0 NA R (>= 3.2) ellipsis, magrittr, rlang, tibble NA covr, ggplot2, testthat, readr, knitr, rmarkdown, dplyr NA GPL-3 NA NA NA NA no 4.0.0
foreach foreach /usr/lib/R/site-library 1.5.0 NA R (>= 2.5.0) codetools, utils, iterators NA randomForest, doMC, doParallel, testthat, knitr, rmarkdown NA Apache License (== 2.0) NA NA NA NA no 4.0.0
foreign foreign /usr/lib/R/site-library 0.8-80 recommended R (>= 4.0.0) methods, utils, stats NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
formatR formatR /usr/lib/R/site-library 1.7 NA R (>= 3.0.2) NA NA codetools, shiny, testit, rmarkdown, knitr NA GPL NA NA NA NA no 4.0.0
fpc fpc /usr/lib/R/site-library 2.2-7 NA R (>= 2.0) MASS, cluster, mclust, flexmix, prabclus, class, diptest, robustbase, kernlab, grDevices, graphics, methods, stats, utils, parallel NA tclust, pdfCluster, EMMIXskew, mvtnorm NA GPL NA NA NA NA no 4.0.0
freetypeharfbuzz freetypeharfbuzz /usr/lib/R/site-library 0.2.5 NA R (>= 3.2) fontquiver NA covr, testthat NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.0
fs fs /usr/lib/R/site-library 1.4.2 NA R (>= 3.1) methods NA testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon, rmarkdown, knitr, withr, spelling NA GPL-3 NA NA NA NA yes 4.0.0
funModeling funModeling /usr/lib/R/site-library 1.9.4 NA R (>= 3.4.0), Hmisc (>= 3.17.1) ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr, lazyeval, utils, RColorBrewer, moments, entropy, cli, stringr NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 4.0.0
furrr furrr /usr/lib/R/site-library 0.1.0 NA R (>= 3.2.0), future (>= 1.6.2) globals (>= 0.10.3), rlang (>= 0.2.0), purrr (>= 0.2.4) NA listenv (>= 0.6.0), dplyr (>= 0.7.4), testthat NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
futile.logger futile.logger /usr/lib/R/site-library 1.4.3 NA R (>= 3.0.0) utils, lambda.r (>= 1.1.0), futile.options NA testthat, jsonlite NA LGPL-3 NA NA NA NA no 4.0.0
futile.options futile.options /usr/lib/R/site-library 1.0.1 NA R (>= 2.8.0) NA NA NA NA LGPL-3 NA NA NA NA no 4.0.0
future future /usr/lib/R/site-library 1.18.0 NA NA digest, globals (>= 0.12.5), listenv (>= 0.8.0), parallel, utils NA RhpcBLASctl, R.rsp, markdown NA LGPL (>= 2.1) NA NA NA NA no 4.0.2
gWidgets gWidgets /usr/lib/R/site-library 0.0-54.2 NA methods, utils NA NA gWidgetstcltk NA GPL (>= 2) NA NA NA NA no 4.0.0
gam gam /usr/lib/R/site-library 1.20 NA R (>= 3.5.0),stats, splines, foreach NA NA akima, testthat NA GPL-2 NA NA NA NA yes 4.0.0
gargle gargle /usr/lib/R/site-library 0.5.0 NA R (>= 3.2) fs (>= 1.3.1), glue (>= 1.3.0), httr (>= 1.4.0), jsonlite, rlang (>= 0.4.2), stats, withr NA covr, knitr, rmarkdown, sodium, spelling, testthat (>= 2.3.2) NA MIT + file LICENSE NA NA NA NA no 4.0.0
gbm gbm /usr/lib/R/site-library 2.1.8 NA R (>= 2.9.0) lattice, parallel, survival NA covr, gridExtra, knitr, pdp, RUnit, splines, tinytest, vip, viridis NA GPL (>= 2) | file LICENSE NA NA NA NA yes 4.0.2
gclus gclus /usr/lib/R/site-library 1.3.2 NA R (>= 2.10), cluster NA NA knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 4.0.0
gdata gdata /usr/lib/R/site-library 2.18.0 NA R (>= 2.3.0) gtools, stats, methods, utils NA RUnit NA GPL-2 NA NA NA NA no 4.0.0
gdtools gdtools /usr/lib/R/site-library 0.2.2 NA NA Rcpp (>= 0.12.12), systemfonts (>= 0.1.1) Rcpp htmltools, testthat, fontquiver (>= 0.2.0), curl NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.0
geepack geepack /usr/lib/R/site-library 1.3-1 NA R (>= 3.5.0), methods MASS, broom, magrittr NA NA NA GPL (>= 3) NA NA NA NA yes 4.0.0
genefilter genefilter /usr/lib/R/site-library 1.70.0 NA NA BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival NA class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr NA Artistic-2.0 NA NA NA NA yes 4.0.0
geneplotter geneplotter /usr/lib/R/site-library 1.66.0 NA R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils NA Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db NA Artistic-2.0 NA NA NA NA no 4.0.0
generics generics /usr/lib/R/site-library 0.0.2 NA R (>= 3.1) methods NA covr, pkgload, testthat, tibble NA GPL-2 NA NA NA NA no 4.0.0
genetics genetics /usr/lib/R/site-library 1.3.8.1.2 NA combinat, gdata, gtools, MASS, mvtnorm NA NA NA NA GPL NA NA NA NA no 4.0.0
getopt getopt /usr/lib/R/site-library 1.20.3 NA NA stats NA covr, testthat NA GPL (>= 2) NA NA NA NA no 4.0.0
ggbeeswarm ggbeeswarm /usr/lib/R/site-library 0.6.0 NA R (>= 3.0.0), ggplot2 (>= 2.0) beeswarm, vipor NA gridExtra NA GPL (>= 2) NA NA NA NA no 4.0.0
ggbiplot ggbiplot /usr/lib/R/site-library 0.55 NA ggplot2, plyr, scales, grid NA NA NA NA GPL-2 NA NA NA NA no 4.0.0
ggdendro ggdendro /usr/lib/R/site-library 0.1-20 NA NA MASS, ggplot2(>= 0.9.2) NA rpart(>= 4.0-0), tree, testthat, knitr, cluster, scales NA GPL-2 | GPL-3 NA NA NA NA no 4.0.0
ggforce ggforce /usr/lib/R/site-library 0.3.2 NA ggplot2 (>= 3.0.0), R (>= 3.3.0) Rcpp (>= 0.12.2), grid, scales, MASS, tweenr (>= 0.1.5), gtable, rlang, polyclip, stats, grDevices, tidyselect, withr, utils Rcpp, RcppEigen sessioninfo, concaveman, deldir, reshape2, units (>= 0.4-6), covr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
ggplot2 ggplot2 /usr/lib/R/site-library 3.3.2 NA R (>= 3.2) digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband, MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble, withr (>= 2.0.0) NA covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, mapproj, maps, maptools, multcomp, munsell, nlme, profvis, quantreg, RColorBrewer, rgeos, rmarkdown, rpart, sf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0), vdiffr (>= 0.3.0) sp GPL-2 | file LICENSE NA NA NA NA no 4.0.0
ggplot2movies ggplot2movies /usr/lib/R/site-library 0.0.1 NA R (>= 2.10.0) NA NA NA NA GPL-3 NA NA NA NA no 4.0.0
ggplotify ggplotify /usr/lib/R/site-library 0.0.5 NA R (>= 3.4.0) ggplot2, graphics, grDevices, grid, gridGraphics, rvcheck NA colorspace, cowplot, ggimage, knitr, lattice, prettydoc, vcd NA Artistic-2.0 NA NA NA NA no 4.0.0
ggpubr ggpubr /usr/lib/R/site-library 0.4.0 NA R (>= 3.1.0), ggplot2 ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>= 0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom, rlang, rstatix (>= 0.6.0), tibble, magrittr NA grDevices, knitr, RColorBrewer, gtable NA GPL-2 NA NA NA NA no 4.0.0
ggraph ggraph /usr/lib/R/site-library 2.0.3 NA R (>= 2.10), ggplot2 (>= 3.0.0) Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>= 1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats, viridis, rlang, tidygraph, graphlayouts (>= 0.5.0) Rcpp network, knitr, rmarkdown, purrr, tibble, seriation, deldir, gganimate NA MIT + file LICENSE NA NA NA NA yes 4.0.0
ggraptR ggraptR /usr/lib/R/site-library 1.3 NA dplyr (>= 0.7.5), ggplot2 (>= 2.2.0), pacman (>= 0.4.6), purrr(>= 0.2.4), shiny (>= 0.12.2) NA NA knitr, markdown NA GPL (>= 2) NA NA NA NA no 4.0.0
ggrepel ggrepel /usr/lib/R/site-library 0.8.2 NA R (>= 3.0.0), ggplot2 (>= 2.2.0) grid, Rcpp, scales (>= 0.3.0) Rcpp knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.0
ggridges ggridges /usr/lib/R/site-library 0.5.2 NA R (>= 3.2) ggplot2 (>= 3.0.0), grid (>= 3.0.0), plyr (>= 1.8.0), scales (>= 0.4.1), withr (>= 2.1.1) NA covr, dplyr, patchwork, ggplot2movies, forcats, knitr, rmarkdown, testthat, vdiffr NA GPL-2 | file LICENSE NA NA NA NA no 4.0.0
ggsci ggsci /usr/lib/R/site-library 2.9 NA R (>= 3.0.2) grDevices, scales, ggplot2 (>= 2.0.0) NA knitr, rmarkdown, gridExtra, reshape2 NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
ggsignif ggsignif /usr/lib/R/site-library 0.6.0 NA NA ggplot2 (>= 2.0.0) NA testthat, knitr, rmarkdown NA GPL-3 NA NA NA NA no 4.0.0
ggthemes ggthemes /usr/lib/R/site-library 4.2.0 NA R (>= 3.3.0) ggplot2 (>= 3.0.0), graphics, grid, methods, purrr, scales, stringr, tibble NA dplyr, covr, extrafont, glue, knitr, lattice, lintr, maps, mapproj, pander, rlang, rmarkdown, spelling, testthat, tidyr, vdiffr, withr NA GPL-2 NA NA NA NA no 4.0.0
gh gh /usr/lib/R/site-library 1.1.0 NA NA cli, ini, jsonlite, httr (>= 1.2) NA covr, keyring, pingr, testthat, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
git2r git2r /usr/lib/R/site-library 0.27.1 NA R (>= 3.1) graphics, utils NA getPass NA GPL-2 NA NA NA NA yes 4.0.0
gld gld /usr/lib/R/site-library 2.6.2 NA NA stats, graphics, e1071, lmom NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
glmnet glmnet /usr/lib/R/site-library 4.0-2 NA R (>= 3.6.0), Matrix (>= 1.0-6) methods, utils, foreach, shape, survival NA knitr, lars, testthat NA GPL-2 NA NA NA NA yes 4.0.0
globals globals /usr/lib/R/site-library 0.12.5 NA R (>= 3.1.2) codetools NA NA NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
glue glue /usr/lib/R/site-library 1.4.1 NA R (>= 3.1) methods NA testthat, covr, magrittr, crayon, knitr, rmarkdown, DBI, RSQLite, R.utils, forcats, microbenchmark, rprintf, stringr, ggplot2, dplyr, withr, vctrs (>= 0.3.0) NA MIT + file LICENSE NA NA NA NA yes 4.0.0
gmailr gmailr /usr/lib/R/site-library 1.0.0 NA R (>= 3.0.0) base64enc, crayon, gargle, httr, jsonlite, lifecycle, magrittr, mime, rematch2 NA covr, knitr, methods, sodium, rmarkdown, testthat, xml2 NA MIT + file LICENSE NA NA NA NA no 4.0.0
goftest goftest /usr/lib/R/site-library 1.2-2 NA R (>= 3.3) stats NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
gower gower /usr/lib/R/site-library 0.2.2 NA NA NA NA tinytest (>= 0.9.3), NA GPL-3 NA NA NA NA yes 4.0.0
gplots gplots /usr/lib/R/site-library 3.0.4 NA R (>= 3.0) gtools, gdata, stats, caTools, KernSmooth NA grid, MASS, knitr NA GPL-2 NA NA NA NA no 4.0.0
gpuR gpuR /usr/lib/R/site-library 2.0.3 NA R (>= 3.0.2), methods, utils Rcpp (>= 0.12.15), assertive Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RViennaCL (>= 1.7.1.7), BH testthat, knitr NA GPL (>= 2) NA NA NA NA yes 4.0.0
graph graph /usr/lib/R/site-library 1.66.0 NA R (>= 2.10), methods, BiocGenerics (>= 0.13.11) stats, stats4, utils NA SparseM (>= 0.36), XML, RBGL, RUnit, cluster Rgraphviz Artistic-2.0 NA NA NA NA yes 4.0.0
graphlayouts graphlayouts /usr/lib/R/site-library 0.7.0 NA R (>= 3.2.0) igraph, Rcpp Rcpp, RcppArmadillo oaqc, testthat, ggraph, ggplot2, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA yes 4.0.0
gridExtra gridExtra /usr/lib/R/site-library 2.3 NA NA gtable, grid, grDevices, graphics, utils NA ggplot2, egg, lattice, knitr, testthat NA GPL (>= 2) NA NA NA NA no 4.0.0
gridGraphics gridGraphics /usr/lib/R/site-library 0.5-0 NA grid, graphics grDevices NA magick (>= 1.3), pdftools (>= 1.6) NA GPL (>= 2) NA NA NA NA no 4.0.0
gss gss /usr/lib/R/site-library 2.2-2 NA R (>= 3.0.0), stats NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
gsubfn gsubfn /usr/lib/R/site-library 0.7 NA proto NA NA boot, chron, grid, lattice, quantreg, svUnit, tcltk, zoo NA GPL (>= 2) NA NA NA NA no 4.0.0
gtable gtable /usr/lib/R/site-library 0.3.0 NA R (>= 3.0) grid NA covr, testthat, knitr, rmarkdown, ggplot2, profvis NA GPL-2 NA NA NA NA no 4.0.0
gtools gtools /usr/lib/R/site-library 3.8.2 NA methods, stats, utils NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
haven haven /usr/lib/R/site-library 2.3.1 NA R (>= 3.2) forcats (>= 0.2.0), hms, methods, Rcpp (>= 0.11.4), readr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect, vctrs (>= 0.3.0) Rcpp covr, fs, knitr, rmarkdown, testthat, pillar (>= 1.4.0), cli, crayon NA MIT + file LICENSE NA NA NA NA yes 4.0.0
heatmaply heatmaply /usr/lib/R/site-library 1.1.0 NA R (>= 3.0.0), plotly (>= 4.7.1), viridis ggplot2 (>= 2.2.0), dendextend (>= 1.12.0), magrittr (>= 1.0.1), reshape2, scales, seriation, utils, stats, grDevices, methods, colorspace, RColorBrewer, htmlwidgets, webshot, assertthat, egg NA knitr, covr, gplots, tidyselect, rmarkdown, testthat NA GPL-2 | GPL-3 NA NA NA NA no 4.0.0
hexbin hexbin /usr/lib/R/site-library 1.28.1 NA R (>= 2.0.1), methods lattice, grid, graphics, grDevices, stats, utils NA marray, affy, Biobase, limma, knitr NA GPL-2 NA NA NA NA yes 4.0.0
highlight highlight /usr/lib/R/site-library 0.5.0 NA R (>= 3.2) grDevices, tools NA NA NA GPL (>= 3) NA NA NA NA yes 4.0.0
highr highr /usr/lib/R/site-library 0.8 NA R (>= 3.2.3) NA NA knitr, testit NA GPL NA NA NA NA no 4.0.0
hmeasure hmeasure /usr/lib/R/site-library 1.0-2 NA R (>= 2.10) NA NA MASS, class, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
hms hms /usr/lib/R/site-library 0.5.3 NA NA methods, pkgconfig, rlang, vctrs (>= 0.2.1) NA crayon, lubridate, pillar (>= 1.1.0), testthat NA GPL-3 NA NA NA NA no 4.0.0
htmlTable htmlTable /usr/lib/R/site-library 2.0.1 NA NA stringr, knitr (>= 1.6), magrittr (>= 1.5), methods, checkmate, htmlwidgets, htmltools, rstudioapi (>= 0.6) NA testthat, XML, xml2, Hmisc, reshape, rmarkdown, chron, lubridate, tibble, purrr, tidyselect, glue, rlang, tidyr (>= 0.7.2), dplyr (>= 0.7.4) NA GPL (>= 3) NA NA NA NA no 4.0.2
htmltools htmltools /usr/lib/R/site-library 0.5.0 NA R (>= 2.14.1) utils, digest, grDevices, base64enc, rlang NA markdown, testthat, withr, Cairo, ragg knitr GPL (>= 2) NA NA NA NA yes 4.0.0
htmlwidgets htmlwidgets /usr/lib/R/site-library 1.5.1 NA NA grDevices, htmltools (>= 0.3), jsonlite (>= 0.9.16), yaml NA knitr (>= 1.8) shiny (>= 1.1) MIT + file LICENSE NA NA NA NA no 4.0.0
httpcode httpcode /usr/lib/R/site-library 0.3.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
httpuv httpuv /usr/lib/R/site-library 1.5.4 NA R (>= 2.15.1) Rcpp (>= 0.11.0), utils, R6, promises, later (>= 0.8.0) Rcpp, BH, later testthat, callr, curl, websocket NA GPL (>= 2) | file LICENSE NA NA NA NA yes 4.0.0
httr httr /usr/lib/R/site-library 1.4.2 NA R (>= 3.2) curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6 NA covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat (>= 0.8.0), xml2 NA MIT + file LICENSE NA NA NA NA no 4.0.2
hunspell hunspell /usr/lib/R/site-library 3.0 NA R (>= 3.0.2) Rcpp, digest Rcpp (>= 0.12.12) spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr, stopwords, rmarkdown NA GPL-2 | LGPL-2.1 | MPL-1.1 NA NA NA NA yes 4.0.0
hwriter hwriter /usr/lib/R/site-library 1.3.2 NA R (>= 2.6.0) NA NA NA NA LGPL-2.1 NA NA NA NA no 4.0.0
igraph igraph /usr/lib/R/site-library 1.2.5 NA methods graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0), stats, utils NA ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk, testthat, withr NA GPL (>= 2) NA NA NA NA yes 4.0.0
imager imager /usr/lib/R/site-library 0.42.3 NA R (>= 2.10.0),magrittr Rcpp (>= 0.11.5),methods,stringr,png,jpeg,readbitmap,grDevices,purrr,downloader,igraph Rcpp knitr, rmarkdown,ggplot2,dplyr,scales, testthat,OpenMPController,raster,spatstat, magick,Cairo NA LGPL-3 NA NA NA NA yes 4.0.0
import import /usr/lib/R/site-library 1.1.0 NA NA NA NA knitr NA MIT + file LICENSE NA NA NA NA no 4.0.0
imputeMissings imputeMissings /usr/lib/R/site-library 0.0.3 NA NA randomForest,stats NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
inTrees inTrees /usr/lib/R/site-library 1.2 NA NA RRF, arules, gbm, xtable, xgboost, data.table, methods NA NA NA GPL (>= 3) NA NA NA NA no 4.0.0
inflection inflection /usr/lib/R/site-library 1.3.5 NA NA parallel, stats, graphics, grDevices NA knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 4.0.0
influenceR influenceR /usr/lib/R/site-library 0.1.0 NA R (>= 3.2.0) igraph (>= 1.0.1), Matrix (>= 1.1-4), methods, utils NA testthat NA GPL-2 NA NA NA NA yes 4.0.0
ini ini /usr/lib/R/site-library 0.3.1 NA NA NA NA testthat NA GPL-3 NA NA NA NA no 4.0.0
inum inum /usr/lib/R/site-library 1.0-1 NA R (>= 3.3.0) stats, libcoin (>= 1.0-0) NA NA NA GPL-2 NA NA NA NA no 4.0.0
ipred ipred /usr/lib/R/site-library 0.9-9 NA R (>= 2.10) rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim NA mvtnorm, mlbench, TH.data NA GPL (>= 2) NA NA NA NA yes 4.0.0
irlba irlba /usr/lib/R/site-library 2.3.3 NA Matrix stats, methods Matrix NA NA GPL-3 NA NA NA NA yes 4.0.0
isoband isoband /usr/lib/R/site-library 0.2.2 NA NA grid, utils testthat covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf, testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
iterators iterators /usr/lib/R/site-library 1.0.12 NA R (>= 2.5.0), utils NA NA RUnit, foreach NA Apache License (== 2.0) NA NA NA NA no 4.0.0
itertools itertools /usr/lib/R/site-library 0.1-3 NA R (>= 2.14.0), iterators(>= 1.0.0) parallel NA foreach NA GPL-2 NA NA NA NA no 4.0.0
janitor janitor /usr/lib/R/site-library 2.0.1 NA R (>= 3.1.2) dplyr (>= 0.7.0), lifecycle, lubridate, magrittr, purrr, rlang, stringi, stringr, snakecase (>= 0.9.2), tidyselect (>= 1.0.0), tidyr (>= 0.7.0) NA knitr, rmarkdown, sf, testthat, tibble, tidygraph NA MIT + file LICENSE NA NA NA NA no 4.0.0
jomo jomo /usr/lib/R/site-library 2.7-1 NA NA stats, lme4, survival, MASS, ordinal NA mitml NA GPL-2 NA NA NA NA yes 4.0.0
jpeg jpeg /usr/lib/R/site-library 0.1-8.1 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
jsonlite jsonlite /usr/lib/R/site-library 1.7.0 NA methods NA NA httr, curl, plyr, testthat, knitr, rmarkdown, R.rsp, sf, sp NA MIT + file LICENSE NA NA NA NA yes 4.0.0
kableExtra kableExtra /usr/lib/R/site-library 1.1.0 NA R (>= 3.1.0) knitr (>= 1.16), magrittr, stringr (>= 1.0), xml2 (>= 1.1.1), rvest, rmarkdown (>= 1.6.0), readr, scales, viridisLite, stats, grDevices, htmltools, rstudioapi, glue, tools, webshot, digest NA testthat, magick, formattable, dplyr NA MIT + file LICENSE NA NA NA NA no 4.0.0
keras keras /usr/lib/R/site-library 2.3.0.0 NA R (>= 3.2) generics (>= 0.0.1), reticulate (>= 1.10), tensorflow (>= 2.0.0), tfruns (>= 1.0), magrittr, zeallot, methods, R6 NA ggplot2, testthat (>= 2.1.0), knitr, rmarkdown, tfdatasets, jpeg NA MIT + file LICENSE NA NA NA NA no 4.0.0
kernlab kernlab /usr/lib/R/site-library 0.9-29 NA R (>= 2.10) methods, stats, grDevices, graphics NA NA NA GPL-2 NA NA NA NA yes 4.0.0
klaR klaR /usr/lib/R/site-library 0.6-15 NA R (>= 2.10.0), MASS combinat, questionr, grDevices, stats, utils, graphics NA scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071 NA GPL-2 | GPL-3 NA NA NA NA no 4.0.0
km.ci km.ci /usr/lib/R/site-library 0.5-2 NA R (>= 1.8.0), survival, stats NA NA NA NA GPL (>= 2) NA NA NA NA NA 4.0.0
knitcitations knitcitations /usr/lib/R/site-library 1.0.10 NA R (>= 3.0) RefManageR (>= 0.8.2), digest, httr (>= 0.3), methods, utils NA testthat, knitr (>= 1.6) NA MIT + file LICENSE NA NA NA NA no 4.0.0
knitr knitr /usr/lib/R/site-library 1.29 NA R (>= 3.2.3) evaluate (>= 0.10), highr, markdown, stringr (>= 0.6), yaml (>= 2.1.19), methods, xfun (>= 0.15), tools NA formatR, testit, digest, rgl (>= 0.95.1201), codetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1), magick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>= 0.4-1), showtext, tibble, sass, ragg, styler (>= 1.2.0) NA GPL NA NA NA NA no 4.0.0
ks ks /usr/lib/R/site-library 1.11.7 NA R (>= 2.10.0) FNN (>= 1.1), kernlab, KernSmooth (>= 2.22), Matrix, mclust, mgcv, multicool, mvtnorm (>= 1.0-0) NA maps, MASS, misc3d (>= 0.4-0), OceanView, oz, rgl (>= 0.66) NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
labeling labeling /usr/lib/R/site-library 0.3 NA NA NA NA NA NA MIT + file LICENSE | Unlimited NA NA NA NA no 4.0.0
labelled labelled /usr/lib/R/site-library 2.5.0 NA NA haven (>= 2.3.1), dplyr NA testthat, knitr, rmarkdown, questionr, snakecase, utf8 memisc GPL-3 NA NA NA NA no 4.0.0
laeken laeken /usr/lib/R/site-library 0.5.1 NA R (>= 3.2.0) boot, MASS NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
lamW lamW /usr/lib/R/site-library 1.3.3 NA R (>= 3.0.2) Rcpp, RcppParallel (>= 4.3.20) Rcpp, RcppParallel (>= 4.3.20) testthat, covr NA BSD_2_clause + file LICENSE NA NA NA NA yes 4.0.0
lambda.r lambda.r /usr/lib/R/site-library 1.2.4 NA R (>= 3.0.0) formatR NA testit NA LGPL-3 NA NA NA NA no 4.0.0
lars lars /usr/lib/R/site-library 1.2 NA R (>= 2.10) NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
later later /usr/lib/R/site-library 1.1.0.1 NA NA Rcpp (>= 0.12.9), rlang Rcpp, BH knitr, rmarkdown, testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
lattice lattice /usr/lib/R/site-library 0.20-41 recommended R (>= 3.0.0) grid, grDevices, graphics, stats, utils NA KernSmooth, MASS, latticeExtra chron GPL (>= 2) NA NA NA NA yes 4.0.0
latticeExtra latticeExtra /usr/lib/R/site-library 0.6-29 NA R (>= 3.6.0), lattice grid, stats, utils, grDevices, png, jpeg, RColorBrewer NA maps, mapproj, deldir, tripack, quantreg, zoo, MASS, mgcv NA GPL (>= 2) NA NA NA NA no 4.0.0
lava lava /usr/lib/R/site-library 1.6.7 NA R (>= 3.0) grDevices, graphics, methods, numDeriv, stats, survival, SQUAREM, utils NA KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields, foreach, geepack, gof (>= 0.9), graph, igraph (>= 0.6), lava.tobit (>= 0.4.7), lme4, mets (>= 1.1), nlme, optimx, polycor, quantreg, rgl, testthat (>= 0.11), visNetwork, zoo NA GPL-3 NA NA NA NA no 4.0.0
lava.tobit lava.tobit /usr/lib/R/site-library 0.5 NA lava (>= 1.5), mets (>= 1.2.2), mvtnorm, survival NA NA NA NA GPL-3 NA NA NA NA no 4.0.0
lavaan lavaan /usr/lib/R/site-library 0.6-6 NA R(>= 3.4) methods, stats4, stats, utils, graphics, MASS, mnormt, pbivnorm, numDeriv NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
lazyeval lazyeval /usr/lib/R/site-library 0.2.2 NA R (>= 3.1.0) NA NA knitr, rmarkdown (>= 0.2.65), testthat, covr NA GPL-3 NA NA NA NA yes 4.0.0
leaps leaps /usr/lib/R/site-library 3.1 NA NA NA biglm NA GPL (>= 2) NA NA NA NA yes 4.0.0
libcoin libcoin /usr/lib/R/site-library 1.0-5 NA R (>= 3.4.0) stats, mvtnorm mvtnorm coin NA GPL-2 NA NA NA NA yes 4.0.0
lifecycle lifecycle /usr/lib/R/site-library 0.2.0 NA R (>= 3.2) glue, rlang (>= 0.4.0) NA covr, crayon, knitr, rmarkdown, testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 4.0.0
limma limma /usr/lib/R/site-library 3.44.3 NA R (>= 3.6.0) grDevices, graphics, stats, utils, methods NA affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn NA GPL (>=2) NA NA NA NA yes 4.0.2
lintr lintr /usr/lib/R/site-library 2.0.1 NA R (>= 3.2) rex, crayon, codetools, cyclocomp, testthat (>= 2.2.1), digest, rstudioapi (>= 0.2), httr (>= 1.2.1), jsonlite, knitr, stats, utils, xml2 (>= 1.0.0), xmlparsedata (>= 1.0.3) NA rmarkdown, mockery NA MIT + file LICENSE NA NA NA NA no 4.0.0
listenv listenv /usr/lib/R/site-library 0.8.0 NA R (>= 3.1.2) NA NA R.utils, R.rsp, markdown NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
lm.beta lm.beta /usr/lib/R/site-library 1.5-1 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
lme4 lme4 /usr/lib/R/site-library 1.1-23 NA R (>= 3.2.0), Matrix (>= 1.2-1), methods, stats graphics, grid, splines, utils, parallel, MASS, lattice, boot, nlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4), statmod Rcpp (>= 0.10.5), RcppEigen knitr, rmarkdown, PKPDmodels, MEMSS, testthat (>= 0.8.1), ggplot2, mlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR2, numDeriv, car, dfoptim NA GPL (>= 2) NA NA NA NA yes 4.0.0
lmom lmom /usr/lib/R/site-library 2.8 NA R (>= 3.0.0) stats, graphics NA NA NA Common Public License Version 1.0 NA NA NA NA yes 4.0.0
lmtest lmtest /usr/lib/R/site-library 0.9-37 NA R (>= 3.0.0), stats, zoo graphics NA car, strucchange, sandwich, dynlm, stats4, survival, AER NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
locfit locfit /usr/lib/R/site-library 1.5-9.4 NA R (>= 3.5.0) lattice NA interp, gam NA GPL (>= 2) NA NA NA NA yes 4.0.0
logcondens logcondens /usr/lib/R/site-library 2.1.5 NA R (>= 2.10) ks, graphics, stats NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
lsr lsr /usr/lib/R/site-library 0.5 NA NA NA NA NA NA GPL-3 NA NA NA NA no 4.0.0
lubridate lubridate /usr/lib/R/site-library 1.7.9 NA methods, R (>= 3.2) generics, Rcpp (>= 0.12.13) Rcpp covr, knitr, testthat (>= 2.1.0), vctrs (>= 0.3.0) chron, timeDate, tis, zoo GPL (>= 2) NA NA NA NA yes 4.0.0
mRMRe mRMRe /usr/lib/R/site-library 2.1.0 NA survival, igraph, methods NA NA NA NA Artistic-2.0 NA NA NA NA yes 4.0.0
magick magick /usr/lib/R/site-library 2.4.0 NA NA Rcpp (>= 0.12.12), magrittr, curl Rcpp av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, rsvg, webp, pdftools, ggplot2, gapminder, IRdisplay, tesseract (>= 2.0), gifski NA MIT + file LICENSE NA NA NA NA yes 4.0.0
magrittr magrittr /usr/lib/R/site-library 1.5 NA NA NA NA testthat, knitr NA MIT + file LICENSE NA NA NA NA no 4.0.0
manipulateWidget manipulateWidget /usr/lib/R/site-library 0.10.1 NA NA shiny (>= 1.0.3), miniUI, htmltools, htmlwidgets, knitr, methods, tools, base64enc, grDevices, codetools, webshot NA dygraphs, leaflet, plotly, xts, rmarkdown, testthat, covr NA GPL (>= 2) | file LICENSE NA NA NA NA no 4.0.0
mapdata mapdata /usr/lib/R/site-library 2.3.0 NA R (>= 2.14.0), maps (>= 2.0-7) NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
mapproj mapproj /usr/lib/R/site-library 1.2.7 NA R (>= 3.0.0), maps (>= 2.3-0) stats, graphics NA NA NA Lucent Public License NA NA NA NA yes 4.0.0
maps maps /usr/lib/R/site-library 3.3.0 NA R (>= 3.0.0) graphics, utils NA mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, maptools, rnaturalearth NA GPL-2 NA NA NA NA yes 4.0.0
maptools maptools /usr/lib/R/site-library 1.0-1 NA R (>= 2.10), sp (>= 1.0-11) foreign (>= 0.8), methods, grid, lattice, stats, utils, grDevices NA rgeos (>= 0.1-8), spatstat (>= 1.60), PBSmapping, maps, RColorBrewer, raster, polyclip, spatstat.utils gpclib GPL (>= 2) NA NA NA NA yes 4.0.0
markdown markdown /usr/lib/R/site-library 1.1 NA R (>= 2.11.1) utils, xfun, mime (>= 0.3) NA knitr, RCurl NA GPL-2 NA NA NA NA yes 4.0.0
matlab matlab /usr/lib/R/site-library 1.0.2 NA R (>= 2.15) methods NA NA NA Artistic-2.0 NA NA NA NA no 4.0.0
matrixStats matrixStats /usr/lib/R/site-library 0.56.0 NA R (>= 2.12.0) NA NA base64enc, ggplot2, knitr, microbenchmark, R.devices, R.rsp NA Artistic-2.0 NA NA NA NA yes 4.0.0
maxstat maxstat /usr/lib/R/site-library 0.7-25 NA R (>= 1.7.0) exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats, graphics NA TH.data, survival NA GPL (>= 2) NA NA NA NA yes 4.0.0
mboost mboost /usr/lib/R/site-library 2.9-2 NA R (>= 3.2.0), methods, stats, parallel, stabs (>= 0.5-0) Matrix, survival, splines, lattice, nnls, quadprog, utils, graphics, grDevices, partykit (>= 1.2-1) NA TH.data, MASS, fields, BayesX, gbm, mlbench, RColorBrewer, rpart (>= 4.0-3), randomForest, nnet, testthat (>= 0.10.0), kangar00 NA GPL-2 NA NA NA NA yes 4.0.0
mclust mclust /usr/lib/R/site-library 5.4.6 NA R (>= 3.0) stats, utils, graphics, grDevices NA knitr (>= 1.12), rmarkdown (>= 0.9), mix (>= 1.0), geometry (>= 0.3-6), MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
mda mda /usr/lib/R/site-library 0.5-2 NA R (>= 3.5.0), stats, class NA NA earth, testthat NA GPL-2 NA NA NA NA yes 4.0.0
memisc memisc /usr/lib/R/site-library 0.99.25.6 NA R (>= 3.3.0), lattice, stats, methods, utils, MASS grid, repr, data.table NA splines, knitr, rmarkdown, sandwich AER, car, eha, lme4, ordinal, simex, tibble, haven GPL-2 NA NA NA NA yes 4.0.2
memoise memoise /usr/lib/R/site-library 1.1.0 NA NA digest (>= 0.6.3) NA testthat, aws.s3, httr, covr NA MIT + file LICENSE NA NA NA NA no 4.0.0
mets mets /usr/lib/R/site-library 1.2.7.1 NA R (>= 3.5), timereg (>= 1.9.4), lava (>= 1.6.6) mvtnorm, numDeriv, compiler, Rcpp, splines, survival (>= 2.43-1), Rcpp, RcppArmadillo, mvtnorm prodlim, testthat (>= 0.11), ucminf, R.rsp (>= 0.40) NA GPL (>= 2) NA NA NA NA yes 4.0.0
mgcv mgcv /usr/lib/R/site-library 1.8-31 recommended R (>= 2.14.0), nlme (>= 3.1-64) methods, stats, graphics, Matrix, splines, utils NA parallel, survival, MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
OmicSelector.1 OmicSelector /usr/lib/R/site-library 0.1.0 NA R (>= 2.10) dplyr, remotes, devtools, ellipsis, BiocManager, plyr, tibble, tidyr, XML, epiDisplay, rsq, MASS, caret, tidyverse, xtable, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr, data.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise, psych, C50, randomForest, nnet, reticulate, stargazer, ggrepel, classInt, plotly, keras, cutpointr, naniar, visdat, imputeMissings, foreach, deepnet, calibrate, networkD3, VennDiagram, RSNNS, kernlab, car, PairedData, profileR, xgboost, kableExtra, curl, tidyselect, rJava, mice, MatchIt, cluster, Biobase, Biocomb, ComplexHeatmap, GDCRNATools, R.utils, TCGAbiolinks, VIM, circlize, edgeR, magick, mgcv, party, rmarkdown, rpart, sva, devtools, nnet NA knitr, rmarkdown NA License: MIT + file LICENSE NA NA NA NA no 4.0.0
mice mice /usr/lib/R/site-library 3.10.0 NA R (>= 2.10.0) broom, dplyr, generics, graphics, lattice, methods, stats, tidyr, utils Rcpp broom.mixed, knitr, lme4, MASS, mitml, miceadds, nnet, pan, randomForest, rmarkdown, rpart, survival, testthat, lmtest NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.2
microbenchmark microbenchmark /usr/lib/R/site-library 1.4-7 NA NA graphics, stats NA ggplot2, multcomp, RUnit NA BSD_2_clause + file LICENSE NA NA NA NA yes 4.0.0
mime mime /usr/lib/R/site-library 0.9 NA NA tools NA NA NA GPL NA NA NA NA yes 4.0.0
miniUI miniUI /usr/lib/R/site-library 0.1.1.1 NA NA shiny (>= 0.13), htmltools (>= 0.3), utils NA NA NA GPL-3 NA NA NA NA no 4.0.0
minqa minqa /usr/lib/R/site-library 1.2.4 NA NA Rcpp (>= 0.9.10) Rcpp NA NA GPL-2 NA NA NA NA yes 4.0.0
missForest missForest /usr/lib/R/site-library 1.4 NA randomForest,foreach,itertools NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
mitml mitml /usr/lib/R/site-library 0.3-7 NA NA pan, jomo, haven, grDevices, graphics, stats, utils NA mice, miceadds, Amelia, lme4, nlme, geepack, survival, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 4.0.0
mlbench mlbench /usr/lib/R/site-library 2.1-1 NA R (>= 2.10) NA NA lattice NA GPL-2 NA NA NA NA NA 4.0.0
mlr mlr /usr/lib/R/site-library 2.17.1 NA ParamHelpers (>= 1.10), R (>= 3.0.2) backports (>= 1.1.0), BBmisc (>= 1.11), checkmate (>= 1.8.2), data.table (>= 1.12.4), ggplot2, methods, parallelMap (>= 1.3), stats, stringi, survival, utils, XML NA ada, adabag, bartMachine, batchtools, brnn, bst, C50, care, caret (>= 6.0-57), class, clue, cluster, ClusterR, clusterSim (>= 0.44-5), cmaes, cowplot, CoxBoost, crs, Cubist, deepnet, DiceKriging, DiscriMiner, e1071, earth, elasticnet, emoa, evtree, extraTrees, fda.usc, FDboost, FNN, forecast (>= 8.3), fpc, frbs, FSelector, FSelectorRcpp (>= 0.2.1), gbm, GenSA, ggpubr, glmnet, GPfit, h2o (>= 3.6.0.8), Hmisc, hrbrthemes, irace (>= 2.0), kernlab, kknn, klaR, knitr, laGP, LiblineaR, lintr (>= 1.0.0.9001), MASS, mboost, mco, mda, memoise, mlbench, mldr, mlrMBO, mmpf, modeltools, mRMRe, neuralnet, nnet, nodeHarvest (>= 0.7-3), numDeriv, pamr, pander, party, penalized (>= 0.9-47), pls, PMCMR (>= 4.1), praznik (>= 5.0.0), randomForest, randomForestSRC (>= 2.7.0), ranger (>= 0.8.0), rappdirs, refund, rex, rFerns, rgenoud, rknn, rmarkdown, ROCR, rotationForest, rpart, RRF, rrlda, rsm, RSNNS, rucrdtw, RWeka, sda, sf, smoof, sparseLDA, stepPlr, survAUC, svglite, SwarmSVM, testthat, tgp, TH.data, tidyr, tsfeatures, vdiffr, wavelets, xgboost (>= 0.7) NA BSD_2_clause + file LICENSE NA NA NA NA yes 4.0.0
mnormt.1 mnormt /usr/lib/R/site-library 2.0.1 NA R (>= 4.0.0) tmvnsim (>= 1.0-2) NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
mockery mockery /usr/lib/R/site-library 0.4.2 NA NA testthat NA knitr, rmarkdown (>= 1.0), R6 NA MIT + file LICENSE NA NA NA NA no 4.0.0
mockr mockr /usr/lib/R/site-library 0.1 NA NA lazyeval NA testthat, covr NA GPL-3 NA NA NA NA no 4.0.0
modelr modelr /usr/lib/R/site-library 0.1.8 NA R (>= 3.2) broom, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble, tidyr (>= 0.8.0), tidyselect, vctrs NA compiler, covr, ggplot2, testthat NA GPL-3 NA NA NA NA no 4.0.0
modeltools modeltools /usr/lib/R/site-library 0.2-23 NA stats, stats4 methods NA NA NA GPL-2 NA NA NA NA no 4.0.0
moments moments /usr/lib/R/site-library 0.14 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
mstate mstate /usr/lib/R/site-library 0.2.12 NA survival (>= 3.1) RColorBrewer NA cmprsk NA GPL (>= 2) NA NA NA NA yes 4.0.0
multcomp multcomp /usr/lib/R/site-library 1.4-13 NA stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4), TH.data (>= 1.0-2) sandwich (>= 2.3-0), codetools NA lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign, xtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>= 0.2-5) NA GPL-2 NA NA NA NA no 4.0.0
multicool multicool /usr/lib/R/site-library 0.1-11 NA methods, Rcpp (>= 0.11.2) NA Rcpp NA NA GPL-2 NA NA NA NA yes 4.0.0
munsell munsell /usr/lib/R/site-library 0.5.0 NA NA colorspace, methods NA ggplot2, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
mvtnorm mvtnorm /usr/lib/R/site-library 1.1-1 NA R(>= 3.5.0) stats, methods NA NA NA GPL-2 NA NA NA NA yes 4.0.0
naniar naniar /usr/lib/R/site-library 0.5.2 NA R (>= 3.1.2) dplyr, ggplot2, purrr, tidyr, tibble (>= 2.0.0), magrittr, stats, visdat, rlang, forcats, viridis, glue, UpSetR NA knitr, rmarkdown, testthat (>= 2.1.0), rpart, rpart.plot, covr, gridExtra, wakefield, vdiffr, here, simputation, imputeTS, gdtools, Hmisc, spelling NA MIT + file LICENSE NA NA NA NA no 4.0.0
networkD3 networkD3 /usr/lib/R/site-library 0.4 NA R (>= 3.0.0) htmlwidgets (>= 0.3.2), igraph, magrittr NA htmltools (>= 0.2.6), jsonlite, knitr, shiny GPL (>= 3) NA NA NA NA no 4.0.0
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nlme nlme /usr/lib/R/site-library 3.1-148 recommended R (>= 3.4.0) graphics, stats, utils, lattice NA Hmisc, MASS NA GPL (>= 2) | file LICENCE NA NA NA NA yes 4.0.0
nloptr nloptr /usr/lib/R/site-library 1.2.2.2 NA NA NA NA testthat (>= 0.8.1), knitr, rmarkdown, inline (>= 0.3.14) NA LGPL-3 NA NA NA NA yes 4.0.0
nnet nnet /usr/lib/R/site-library 7.3-14 recommended R (>= 3.0.0), stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
nnls nnls /usr/lib/R/site-library 1.4 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA NA 4.0.0
nor1mix nor1mix /usr/lib/R/site-library 1.3-0 NA NA stats, graphics NA cluster NA GPL (>= 2) NA NA NA NA no 4.0.0
nortest nortest /usr/lib/R/site-library 1.0-4 NA NA stats NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
np np /usr/lib/R/site-library 0.60-10 NA NA boot, cubature, methods, quadprog, quantreg, stats NA MASS NA GPL NA NA NA NA yes 4.0.0
numDeriv numDeriv /usr/lib/R/site-library 2016.8-1.1 NA R (>= 2.11.1) NA NA NA NA GPL-2 NA NA NA NA no 4.0.0
nycflights13 nycflights13 /usr/lib/R/site-library 1.0.1 NA R (>= 3.2) tibble NA dplyr NA CC0 NA NA NA NA no 4.0.0
olsrr olsrr /usr/lib/R/site-library 0.5.3 NA R(>= 3.3) car, data.table, ggplot2, goftest, graphics, gridExtra, nortest, Rcpp, stats, utils Rcpp covr, descriptr, knitr, rmarkdown, testthat, vdiffr, xplorerr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
openintro openintro /usr/lib/R/site-library 2.0.0 NA R (>= 2.10), airports, cherryblossom, usdata ggplot2 (>= 2.2.1), graphics, rmarkdown, tibble NA broom, dplyr, forcats, lubridate, tidyr, knitr NA GPL-3 NA NA NA NA no 4.0.0
openssl openssl /usr/lib/R/site-library 1.4.2 NA NA askpass NA testthat (>= 2.1.0), digest, knitr, rmarkdown, jsonlite, jose, sodium NA MIT + file LICENSE NA NA NA NA yes 4.0.0
openxlsx openxlsx /usr/lib/R/site-library 4.1.5 NA R (>= 3.3.0) grDevices, methods, Rcpp, stats, utils, zip, stringi Rcpp knitr, testthat, roxygen2 NA MIT + file LICENSE NA NA NA NA yes 4.0.0
optimx optimx /usr/lib/R/site-library 2020-4.2 NA NA numDeriv NA knitr, rmarkdown, setRNG, BB, ucminf, minqa, dfoptim, lbfgsb3c, lbfgs, subplex NA GPL-2 NA NA NA NA no 4.0.0
optparse optparse /usr/lib/R/site-library 1.6.6 NA R (>= 2.9.0) methods, getopt (>= 1.20.2) NA covr, knitr (>= 1.15.19), stringr, testthat NA GPL (>= 2) NA NA NA NA no 4.0.0
ordinal ordinal /usr/lib/R/site-library 2019.12-10 NA R (>= 2.13.0), stats, methods ucminf, MASS, Matrix, numDeriv NA lme4, nnet, xtable, testthat (>= 0.8), tools NA GPL (>= 2) NA NA NA NA yes 4.0.0
ordinalNet ordinalNet /usr/lib/R/site-library 2.9 NA NA stats, graphics NA testthat (>= 1.0.2), MASS (>= 7.3-45), glmnet (>= 2.0-5), penalized (>= 0.9-50), VGAM (>= 1.0-3), rms (>= 5.1-0) NA MIT + file LICENSE NA NA NA NA yes 4.0.2
org.Hs.eg.db org.Hs.eg.db /usr/lib/R/site-library 3.11.4 NA R (>= 2.7.0), methods, AnnotationDbi (>= 1.49.2) methods, AnnotationDbi NA DBI, annotate, RUnit NA Artistic-2.0 NA NA NA NA no 4.0.0
oro.dicom oro.dicom /usr/lib/R/site-library 0.5.3 NA R (>= 2.14.0) utils, oro.nifti (>= 0.4.0) NA testthat, hwriter NA BSD_3_clause + file LICENSE NA NA NA NA no 4.0.0
oro.nifti oro.nifti /usr/lib/R/site-library 0.10.3 NA R (>= 2.14.0) stats, bitops, splines, graphics, grDevices, methods, utils, abind, RNifti (>= 0.9.0), rticles NA XML, testthat, covr, knitr, rmarkdown fmri, oro.dicom BSD_3_clause + file LICENSE NA NA NA NA no 4.0.0
pROC pROC /usr/lib/R/site-library 1.16.2 NA R (>= 2.14) methods, plyr, Rcpp (>= 0.11.1) Rcpp microbenchmark, tcltk, MASS, logcondens, doParallel, testthat, vdiffr, ggplot2 NA GPL (>= 3) NA NA NA NA yes 4.0.0
pacman pacman /usr/lib/R/site-library 0.5.1 NA R (>= 3.5.0) remotes, methods, stats, utils NA BiocManager, knitr, lattice, testthat (>= 0.9.0), XML NA GPL-2 NA NA NA NA no 4.0.0
pamr pamr /usr/lib/R/site-library 1.56.1 NA R (>= 2.10), cluster, survival NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
pan pan /usr/lib/R/site-library 1.6 NA NA NA NA mitools, lme4 NA GPL-3 NA no NA NA yes 4.0.0
pander pander /usr/lib/R/site-library 0.6.3 NA R (>= 2.15.0) grDevices, graphics, methods, utils, stats, digest, tools, Rcpp Rcpp grid, lattice, ggplot2 (>= 0.9.2), sylly, sylly.en, futile.logger, survival, microbenchmark, zoo, nlme, descr, MASS, knitr, rmarkdown, tables, reshape, memisc, Epi, randomForest, tseries, gtable, rms, forecast, data.table NA AGPL-3 | file LICENSE NA NA NA NA yes 4.0.0
parallelMap parallelMap /usr/lib/R/site-library 1.5.0 NA R (>= 3.0.0) BBmisc (>= 1.8), checkmate (>= 1.8.0), parallel, stats, utils NA BatchJobs (>= 1.8), batchtools (>= 0.9.6), data.table, Rmpi, rpart, snow, testthat NA BSD_2_clause + file LICENSE NA NA NA NA no 4.0.0
parsedate parsedate /usr/lib/R/site-library 1.2.0 NA NA rematch2 NA covr, testthat, withr NA GPL-2 NA NA NA NA yes 4.0.0
parsetools parsetools /usr/lib/R/site-library 0.1.3 NA NA methods, utils NA covr, knitr, rmarkdown, testthat NA GPL-2 NA NA NA NA no 4.0.0
party party /usr/lib/R/site-library 1.3-5 NA R (>= 3.0.0), methods, grid, stats, mvtnorm (>= 1.0-2), modeltools (>= 0.2-21), strucchange survival (>= 2.37-7), coin (>= 1.1-0), zoo, sandwich (>= 1.1-1) mvtnorm TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd, ipred, varImp NA GPL-2 NA NA NA NA yes 4.0.0
partykit partykit /usr/lib/R/site-library 1.2-9 NA R (>= 3.5.0), graphics, grid, libcoin (>= 1.0-0), mvtnorm grDevices, stats, utils, survival, Formula (>= 1.2-1), inum (>= 1.0-0), rpart (>= 4.1-11) NA XML, pmml, rJava, sandwich, strucchange, vcd, AER, mlbench, TH.data (>= 1.0-3), coin (>= 1.1-0), RWeka (>= 0.4-19), datasets, parallel, psychotools (>= 0.3-0), psychotree, party (>= 1.3-0) NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.2
pastecs pastecs /usr/lib/R/site-library 1.3.21 NA NA boot, stats, graphics, utils, grDevices NA svUnit, covr NA GPL-2 NA NA NA NA no 4.0.0
pathview pathview /usr/lib/R/site-library 1.28.1 NA R (>= 2.10) KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils NA gage, org.Mm.eg.db, RUnit, BiocGenerics NA GPL (>=3.0) NA NA NA NA no 4.0.2
pbapply pbapply /usr/lib/R/site-library 1.4-2 NA R (>= 3.2.0) parallel NA NA NA GPL-2 NA NA NA NA no 4.0.0
pbivnorm pbivnorm /usr/lib/R/site-library 0.6.0 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
pbkrtest pbkrtest /usr/lib/R/site-library 0.4-8.6 NA R (>= 3.6.0), lme4 (>= 1.1.10) Matrix (>= 1.2.3), parallel, magrittr, MASS, methods NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
pca3d pca3d /usr/lib/R/site-library 0.10.1 NA R (>= 2.10) rgl,ellipse NA knitr NA GPL-2 NA NA NA NA no 4.0.0
pec pec /usr/lib/R/site-library 2019.11.03 NA R (>= 2.9.0), prodlim (>= 1.4.9) foreach (>= 1.4.2), rms (>= 4.2-0), survival (>= 2.37-7), timereg (>= 1.8.9) NA randomForestSRC, party, cmprsk (>= 2.2-7), rpart, CoxBoost, crrstep, riskRegression (>= 1.0.8), lava (>= 1.4.1), Hmisc (>= 3.14-4) NA GPL (>= 2) NA NA NA NA yes 4.0.0
permute permute /usr/lib/R/site-library 0.9-5 NA R (>= 2.14.0) stats NA vegan (>= 2.0-0), testthat (>= 0.5), parallel NA GPL-2 NA NA NA NA no 4.0.0
pheatmap pheatmap /usr/lib/R/site-library 1.0.12 NA R (>= 2.0) grid, RColorBrewer, scales, gtable, stats, grDevices, graphics NA NA NA GPL-2 NA NA NA NA no 4.0.0
pillar pillar /usr/lib/R/site-library 1.4.6 NA NA cli, crayon (>= 1.3.4), ellipsis, fansi, lifecycle, rlang (>= 0.3.0), utf8 (>= 1.1.0), vctrs (>= 0.2.0) NA bit64, knitr, lubridate, testthat (>= 2.0.0), withr NA GPL-3 NA NA NA NA no 4.0.2
pingr pingr /usr/lib/R/site-library 2.0.1 NA NA processx, utils NA covr, testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
pinp pinp /usr/lib/R/site-library 0.0.9 NA NA rmarkdown, knitr NA NA NA GPL-3 NA NA NA NA no 4.0.0
pixmap pixmap /usr/lib/R/site-library 0.4-11 NA methods NA NA NA NA GPL-2 NA NA NA NA NA 4.0.0
pkgbuild pkgbuild /usr/lib/R/site-library 1.1.0 NA R (>= 3.1) callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6, rprojroot, withr (>= 2.1.2) NA Rcpp, cpp11, testthat, covr NA GPL-3 NA NA NA NA no 4.0.2
pkgcond pkgcond /usr/lib/R/site-library 0.1.0 NA R(>= 3.5.0) methods NA covr, testthat assertthat GPL-2 NA NA NA NA no 4.0.0
pkgconfig pkgconfig /usr/lib/R/site-library 2.0.3 NA NA utils NA covr, testthat, disposables (>= 1.0.3) NA MIT + file LICENSE NA NA NA NA no 4.0.0
pkgdown pkgdown /usr/lib/R/site-library 1.5.1 NA R (>= 3.1.0) callr (>= 2.0.2), cli, crayon, desc, digest, evaluate, fs (>= 1.3.0), fansi, highlight, httr, magrittr, MASS, memoise, openssl, purrr, processx, rematch2, rlang (>= 0.3.0), rmarkdown (>= 1.1.9007), rstudioapi, tibble, tools, whisker, withr, xml2 (>= 1.3.1), yaml NA covr, htmlwidgets, jsonlite, knitr, leaflet, pkgload (>= 1.0.2), testthat (>= 2.1.0), rticles, rsconnect NA MIT + file LICENSE NA NA NA NA no 4.0.0
pkgload pkgload /usr/lib/R/site-library 1.1.0 NA NA cli, crayon, desc, methods, pkgbuild, rlang, rprojroot, rstudioapi, utils, withr NA bitops, covr, Rcpp, testthat NA GPL-3 NA NA NA NA yes 4.0.0
plogr plogr /usr/lib/R/site-library 0.2.0 NA NA NA NA Rcpp NA MIT + file LICENSE NA NA NA NA no 4.0.0
plotly plotly /usr/lib/R/site-library 4.9.2.1 NA R (>= 3.2.0), ggplot2 (>= 3.0.0) tools, scales, httr, jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.3), tidyr, hexbin, RColorBrewer, dplyr, tibble, lazyeval (>= 0.2.0), rlang, crosstalk, purrr, data.table, promises NA MASS, maps, ggthemes, GGally, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, vdiffr, Cairo, broom, webshot, listviewer, dendextend, sf, maptools, rgeos, png, IRdisplay, processx, plotlyGeoAssets, forcats NA MIT + file LICENSE NA NA NA NA no 4.0.0
plotmo plotmo /usr/lib/R/site-library 3.5.7 NA R (>= 3.4.0), Formula (>= 1.2-3), plotrix, TeachingDemos NA NA C50 (>= 0.1.0-24), earth (>= 5.1.0), gbm (>= 2.1.1), glmnet (>= 2.0.5), glmnetUtils (>= 1.0.3), MASS (>= 7.3-45), mlr (>= 2.12.1), neuralnet (>= 1.33), partykit (>= 1.2-2), pre (>= 0.5.0), rpart (>= 4.1-10), rpart.plot (>= 2.1.0) NA GPL-3 NA NA NA NA no 4.0.0
plotrix plotrix /usr/lib/R/site-library 3.7-8 NA R (>= 3.5.0) grDevices, graphics, stats, utils NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
pls pls /usr/lib/R/site-library 2.7-2 NA R (>= 2.10) grDevices, graphics, methods, stats NA MASS, parallel, Rmpi, testthat, RUnit NA GPL-2 NA NA NA NA no 4.0.0
plyr plyr /usr/lib/R/site-library 1.8.6 NA R (>= 3.1.0) Rcpp (>= 0.11.0) Rcpp abind, covr, doParallel, foreach, iterators, itertools, tcltk, testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
pmml pmml /usr/lib/R/site-library 2.3.1 NA XML methods, stats, utils, stringr NA ada, amap, arules, caret, clue, data.table, forecast, gbm, glmnet, Matrix, neighbr, nnet, rpart, randomForestSRC (<= 2.5.0), randomForest, rattle, kernlab, e1071, testthat, survival, xgboost, knitr, rmarkdown, covr NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
png png /usr/lib/R/site-library 0.1-7 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
polspline polspline /usr/lib/R/site-library 1.1.19 NA NA stats, graphics NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
polyclip polyclip /usr/lib/R/site-library 1.10-0 NA R (>= 3.0.0) NA NA NA NA BSL NA NA NA NA yes 4.0.0
polycor polycor /usr/lib/R/site-library 0.7-10 NA R (>= 3.3.0) stats, mvtnorm, Matrix NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
polynom polynom /usr/lib/R/site-library 1.4-0 NA NA stats, graphics NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 4.0.0
postlogic postlogic /usr/lib/R/site-library 0.1.0.1 NA NA NA NA testthat, covr NA GPL-2 NA NA NA NA no 4.0.0
prabclus prabclus /usr/lib/R/site-library 2.3-2 NA R (>= 2.10), MASS, mclust NA NA spdep, spatialreg, bootstrap, maptools, foreign, mvtnorm NA GPL NA NA NA NA no 4.0.0
praise praise /usr/lib/R/site-library 1.0.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
prediction prediction /usr/lib/R/site-library 0.3.14 NA R (>= 3.5.0) utils, stats, data.table NA datasets, methods, testthat AER, aod, betareg, biglm, brglm, caret, crch, e1071, earth, ff, ffbase, gam (>= 1.15), gee, glmnet, glmx, kernlab, lme4, MASS, mclogit, mda, mlogit, MNP, nlme, nnet, ordinal, plm, pscl, quantreg, rpart, sampleSelection, speedglm, survey (>= 3.31-5), survival, truncreg, VGAM MIT + file LICENSE NA NA NA NA no 4.0.0
prettyunits prettyunits /usr/lib/R/site-library 1.1.1 NA NA NA NA codetools, covr, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
processx processx /usr/lib/R/site-library 3.4.3 NA NA ps (>= 1.2.0), R6, utils NA callr (>= 3.2.0), codetools, covr, crayon, curl, debugme, parallel, testthat, withr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
prodlim prodlim /usr/lib/R/site-library 2019.11.13 NA R (>= 2.9.0) Rcpp (>= 0.11.5), stats, grDevices, graphics, survival, KernSmooth, lava Rcpp NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
profileModel profileModel /usr/lib/R/site-library 0.6.0 NA R (>= 2.6.0) NA NA MASS, gnm NA GPL (>= 2) NA NA NA NA no 4.0.0
profileR profileR /usr/lib/R/site-library 0.3-5 NA ggplot2, RColorBrewer, reshape, lavaan, R (>= 3.0.0) NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
profmem profmem /usr/lib/R/site-library 0.5.0 NA NA utils NA R.rsp, markdown, microbenchmark NA LGPL (>= 2.1) NA NA NA NA no 4.0.0
profvis profvis /usr/lib/R/site-library 0.3.6 NA R (>= 3.0) htmlwidgets (>= 0.3.2), stringr NA knitr, ggplot2, rmarkdown, testthat, devtools, shiny, htmltools NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.0
progress progress /usr/lib/R/site-library 1.2.2 NA NA hms, prettyunits, R6, crayon NA Rcpp, testthat, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
promises promises /usr/lib/R/site-library 1.1.1 NA NA R6, Rcpp, later, rlang, stats, magrittr later, Rcpp testthat, future, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA yes 4.0.0
proto proto /usr/lib/R/site-library 1.0.0 NA NA NA NA testthat, covr NA GPL-2 NA NA NA NA no 4.0.0
proxy proxy /usr/lib/R/site-library 0.4-24 NA R (>= 3.4.0) stats, utils NA cba NA GPL-2 NA NA NA NA yes 4.0.0
ps ps /usr/lib/R/site-library 1.3.3 NA R (>= 3.1) utils NA callr, covr, curl, pingr, processx (>= 3.1.0), R6, rlang, testthat, tibble NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
pspearman pspearman /usr/lib/R/site-library 0.3-0 NA NA NA NA NA NA GPL-3 NA NA NA NA yes 4.0.0
psych psych /usr/lib/R/site-library 1.9.12.31 NA NA mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme NA psychTools, GPArotation, lavaan, sem, lme4,Rcsdp, graph, Rgraphviz NA GPL (>= 2) NA NA NA NA no 4.0.0
purrr purrr /usr/lib/R/site-library 0.3.4 NA R (>= 3.2) magrittr (>= 1.5), rlang (>= 0.3.1) NA covr, crayon, dplyr (>= 0.7.8), knitr, rmarkdown, testthat, tibble, tidyselect NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.0
purrrogress purrrogress /usr/lib/R/site-library 0.1.1 NA NA R6, assertthat, glue, hms, methods, pkgcond, purrr, testextra, utils, rlang NA covr, datasets, stringi, testthat, tibble dplyr MIT + file LICENSE NA NA NA NA no 4.0.0
pvclust pvclust /usr/lib/R/site-library 2.2-0 NA R (>= 2.10.0) NA NA MASS, parallel NA GPL (>= 2) NA NA NA NA no 4.0.0
qap qap /usr/lib/R/site-library 0.1-1 NA NA NA NA testthat NA GPL-3 NA NA NA NA yes 4.0.0
qtl qtl /usr/lib/R/site-library 1.46-2 NA R (>= 2.14.0) parallel, graphics, stats, utils, grDevices NA testthat NA GPL-3 NA NA NA NA yes 4.0.0
quadprog quadprog /usr/lib/R/site-library 1.5-8 NA R (>= 3.1.0) NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
quantmod quantmod /usr/lib/R/site-library 0.4.17 NA R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods curl NA DBI,RMySQL,RSQLite,timeSeries,XML,downloader,jsonlite(>= 1.1) NA GPL-3 NA NA NA NA no 4.0.0
quantreg quantreg /usr/lib/R/site-library 5.61 NA R (>= 2.6), stats, SparseM methods, graphics, Matrix, MatrixModels, conquer NA tripack, akima, MASS, survival, rgl, logspline, nor1mix, Formula, zoo, R.rsp NA GPL (>= 2) NA NA NA NA yes 4.0.2
questionr questionr /usr/lib/R/site-library 0.7.1 NA R (>= 3.5.0) shiny (>= 1.0.5), miniUI, rstudioapi, highr, styler, classInt, htmltools, graphics, stats, utils, labelled (>= 2.4.0), haven (>= 2.3.0) NA testthat, roxygen2, dplyr, tidyr, janitor, forcats, knitr NA GPL (>= 2) NA NA NA NA no 4.0.0
qvalue qvalue /usr/lib/R/site-library 2.20.0 NA R(>= 2.10) splines, ggplot2, grid, reshape2 NA knitr NA LGPL NA NA NA NA no 4.0.0
qvcalc qvcalc /usr/lib/R/site-library 1.0.2 NA NA NA NA relimp, MASS psychotools, survival GPL-2 | GPL-3 NA NA NA NA no 4.0.0
rARPACK rARPACK /usr/lib/R/site-library 0.11-0 NA NA RSpectra NA Matrix (>= 1.1-0) NA BSD_3_clause + file LICENSE NA NA NA NA no 4.0.0
rJava rJava /usr/lib/R/site-library 0.9-13 NA R (>= 2.5.0), methods NA NA NA NA GPL-2 NA NA NA NA yes 4.0.2
randomForest randomForest /usr/lib/R/site-library 4.6-14 NA R (>= 3.2.2), stats NA NA RColorBrewer, MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
ranger ranger /usr/lib/R/site-library 0.12.1 NA R (>= 3.1) Rcpp (>= 0.11.2), Matrix Rcpp, RcppEigen survival, testthat NA GPL-3 NA NA NA NA yes 4.0.0
rappdirs rappdirs /usr/lib/R/site-library 0.3.1 NA R (>= 2.14), methods NA NA testthat, roxygen2 NA MIT + file LICENSE NA NA NA NA yes 4.0.0
raster raster /usr/lib/R/site-library 3.3-13 NA sp (>= 1.4.1), R (>= 3.5.0) Rcpp, methods Rcpp rgdal (>= 1.5-8), rgeos (>= 0.3-8), ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf, tinytest, gstat, fields NA GPL (>= 3) NA NA NA NA yes 4.0.2
rattle rattle /usr/lib/R/site-library 5.4.0 NA R (>= 3.5.0), tibble, bitops stats, utils, ggplot2, grDevices, graphics, magrittr, methods, stringi, stringr, tidyr, dplyr, XML, rpart.plot NA pmml (>= 1.2.13), colorspace, ada, amap, arules, arulesViz, biclust, cairoDevice, cba, cluster, corrplot, descr, doBy, e1071, ellipse, fBasics, foreign, fpc, gdata, ggdendro, ggraptR, gplots, grid, gridExtra, gtools, hmeasure, Hmisc, kernlab, Matrix, mice, nnet, party, plyr, psych, randomForest, RColorBrewer, readxl, reshape, rggobi, RGtk2, ROCR, RODBC, rpart, scales, SnowballC, survival, timeDate, tm, verification, wskm, xgboost NA GPL (>= 2) NA NA NA NA no 4.0.0
rattle.data rattle.data /usr/lib/R/site-library 1.0.2 NA R (>= 2.10) NA NA rattle NA GPL-3 NA NA NA NA no 4.0.0
rcmdcheck rcmdcheck /usr/lib/R/site-library 1.3.3 NA NA callr (>= 3.1.1.9000), cli (>= 1.1.0), crayon, desc (>= 1.2.0), digest, pkgbuild, prettyunits, R6, rprojroot, sessioninfo (>= 1.1.1), utils, withr, xopen NA covr, knitr, mockery, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
readbitmap readbitmap /usr/lib/R/site-library 0.1.5 NA NA bmp, jpeg, png, tiff NA pixmap, testthat NA GPL (>= 2) NA NA NA NA no 4.0.0
readr readr /usr/lib/R/site-library 1.3.1 NA R (>= 3.1) Rcpp (>= 0.12.0.5), tibble, hms (>= 0.4.1), R6, clipr, crayon, methods Rcpp, BH curl, testthat, knitr, rmarkdown, stringi, covr, spelling NA GPL (>= 2) | file LICENSE NA NA NA NA yes 4.0.0
readxl readxl /usr/lib/R/site-library 1.3.1 NA NA cellranger, Rcpp (>= 0.12.18), tibble (>= 1.3.1), utils progress, Rcpp covr, knitr, rmarkdown, rprojroot (>= 1.1), testthat NA GPL-3 NA NA NA NA yes 4.0.0
rebus rebus /usr/lib/R/site-library 0.1-3 NA R (>= 3.1.0) rebus.base (>= 0.0-3), rebus.datetimes, rebus.numbers, rebus.unicode (>= 0.0-2) NA testthat NA Unlimited NA NA NA NA no 4.0.0
rebus.base rebus.base /usr/lib/R/site-library 0.0-3 NA R (>= 3.1.0) stats NA stringi, testthat NA Unlimited NA NA NA NA no 4.0.0
rebus.datetimes rebus.datetimes /usr/lib/R/site-library 0.0-1 NA R (>= 3.1.0) rebus.base NA stats, testthat NA Unlimited NA NA NA NA no 4.0.0
rebus.numbers rebus.numbers /usr/lib/R/site-library 0.0-1 NA R (>= 3.1.0) rebus.base, utils NA testthat NA Unlimited NA NA NA NA no 4.0.0
rebus.unicode rebus.unicode /usr/lib/R/site-library 0.0-2 NA R (>= 3.1.0) rebus.base (>= 0.0-2) NA stringi NA Unlimited NA NA NA NA no 4.0.0
recipes recipes /usr/lib/R/site-library 0.1.13 NA R (>= 3.1), dplyr generics, glue, gower, ipred, lifecycle, lubridate, magrittr, Matrix, purrr (>= 0.2.3), rlang (>= 0.4.0), stats, tibble, tidyr (>= 1.0.0), tidyselect (>= 0.2.5), timeDate, utils, withr NA covr, ddalpha, dimRed (>= 0.2.2), fastICA, ggplot2, igraph, kernlab, knitr, modeldata, RANN, RcppRoll, rmarkdown, rpart, rsample, RSpectra, testthat (>= 2.1.0), xml2 NA GPL-2 NA NA NA NA no 4.0.0
reghelper reghelper /usr/lib/R/site-library 0.3.6 NA R (>= 3.1.0) ggplot2 (>= 1.0.0), stats, nlme, lme4, utils NA testthat (>= 0.8.1) NA GPL-3 NA NA NA NA no 4.0.0
registry registry /usr/lib/R/site-library 0.5-1 NA R (>= 2.6.0) utils NA NA NA GPL-2 NA NA NA NA no 4.0.0
rematch rematch /usr/lib/R/site-library 1.0.1 NA NA NA NA covr, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
rematch2 rematch2 /usr/lib/R/site-library 2.1.2 NA NA tibble NA covr, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
remote remote /usr/lib/R/site-library 1.2.1 NA R (>= 2.10), Rcpp (>= 0.10.3), raster, methods grDevices, gridExtra, latticeExtra, mapdata, scales, stats, utils Rcpp maps, lattice, grid, sp NA GPL (>= 3) | file LICENSE NA NA NA NA yes 4.0.0
remotes remotes /usr/lib/R/site-library 2.2.0 NA R (>= 3.0.0) methods, stats, tools, utils NA brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr, mockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot, testthat, withr NA GPL (>= 2) NA NA NA NA no 4.0.2
repr repr /usr/lib/R/site-library 1.1.0 NA R (>= 3.0.1) utils, grDevices, htmltools, jsonlite, pillar (>= 1.4.0), base64enc NA methods, highr, Cairo, stringr, testthat, diffobj (>= 0.2.3), leaflet data.table, dplyr, htmlwidgets, vegalite, plotly, geojsonio GPL-3 NA NA NA NA no 4.0.0
reprex reprex /usr/lib/R/site-library 0.3.0 NA R (>= 3.1) callr (>= 2.0.0), clipr (>= 0.4.0), fs, rlang, rmarkdown, utils, whisker, withr NA covr, devtools, fortunes, knitr, miniUI, rprojroot, rstudioapi, shiny, styler (>= 1.0.2), testthat (>= 2.0.0) NA MIT + file LICENSE NA NA NA NA no 4.0.0
repurrrsive repurrrsive /usr/lib/R/site-library 1.0.0 NA R (>= 2.10) tibble, utils NA gapminder, jsonlite, purrr, rprojroot, testthat (>= 2.1.0), wesanderson, xml2 NA CC0 NA NA NA NA no 4.0.0
reshape reshape /usr/lib/R/site-library 0.8.8 NA R (>= 2.6.1) plyr NA NA NA MIT + file LICENSE NA NA NA NA yes 4.0.0
reshape2 reshape2 /usr/lib/R/site-library 1.4.4 NA R (>= 3.1) plyr (>= 1.8.1), Rcpp, stringr Rcpp covr, lattice, testthat (>= 0.8.0) NA MIT + file LICENSE NA NA NA NA yes 4.0.0
reticulate reticulate /usr/lib/R/site-library 1.16 NA R (>= 3.0) graphics, jsonlite, Matrix, methods, rappdirs, Rcpp (>= 0.12.7), utils Rcpp callr, knitr, rmarkdown, testthat NA Apache License 2.0 NA NA NA NA yes 4.0.0
rex rex /usr/lib/R/site-library 1.2.0 NA NA lazyeval NA testthat, knitr, rmarkdown, dplyr, ggplot2, magrittr, Hmisc, stringr, rvest, roxygen2, covr NA MIT + file LICENSE NA NA NA NA no 4.0.0
rgeos rgeos /usr/lib/R/site-library 0.5-3 NA R (>= 3.3.0), methods, sp (>= 1.1-0) utils, stats, graphics sp maptools (>= 0.8-5), testthat, XML, maps, rgdal NA GPL (>= 2) NA NA NA NA yes 4.0.0
rgexf rgexf /usr/lib/R/site-library 0.16.0 NA NA XML, igraph, grDevices, utils, servr NA knitr, rmarkdown, testthat, covr NA MIT + file LICENSE NA NA NA NA no 4.0.0
rgl rgl /usr/lib/R/site-library 0.100.54 NA R (>= 3.2.0) graphics, grDevices, stats, utils, htmlwidgets, htmltools, knitr, jsonlite (>= 0.9.20), shiny, magrittr, crosstalk, manipulateWidget (>= 0.9.0) NA MASS, rmarkdown, deldir, orientlib, lattice, misc3d, rstudioapi, magick, plotrix (>= 3.7-3), tripack, interp, alphashape3d, tcltk NA GPL NA NA NA NA yes 4.0.0
rhub rhub /usr/lib/R/site-library 1.1.1 NA NA assertthat, callr, cli (>= 1.1.0), crayon, desc, digest, httr, jsonlite, parsedate, pillar, prettyunits, processx, R6, rappdirs, rcmdcheck (>= 1.2.1), rematch, tibble, utils, uuid, whoami, withr NA covr, testthat, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA no 4.0.0
rio rio /usr/lib/R/site-library 0.5.16 NA R (>= 2.15.0) tools, stats, utils, foreign, haven (>= 1.1.0), curl (>= 0.6), data.table (>= 1.9.8), readxl (>= 0.1.1), openxlsx, tibble NA datasets, bit64, testthat, knitr, magrittr, clipr, csvy, feather, fst, hexView, jsonlite, readODS (>= 1.6.4), readr, rmatio, xml2 (>= 1.2.0), yaml NA GPL-2 NA NA NA NA no 4.0.0
rjson rjson /usr/lib/R/site-library 0.2.20 NA R (>= 3.1.0) NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
rlang rlang /usr/lib/R/site-library 0.4.7 NA R (>= 3.2.0) NA NA cli, covr, crayon, glue, magrittr, methods, pillar, rmarkdown, testthat (>= 2.3.0), vctrs (>= 0.2.3), withr NA GPL-3 NA NA NA NA yes 4.0.2
rmarkdown rmarkdown /usr/lib/R/site-library 2.3 NA R (>= 3.0) tools, utils, knitr (>= 1.22), yaml (>= 2.1.19), htmltools (>= 0.3.5), evaluate (>= 0.13), base64enc, jsonlite, mime, tinytex (>= 0.11), xfun, methods, stringr (>= 1.2.0) NA shiny (>= 0.11), tufte, testthat, digest, dygraphs, tibble, fs, pkgdown, rsconnect NA GPL-3 NA NA NA NA no 4.0.0
rmdformats rmdformats /usr/lib/R/site-library 0.3.7 NA NA knitr, rmarkdown, bookdown, htmltools NA questionr NA GPL (>= 2) NA NA NA NA no 4.0.0
rmeta rmeta /usr/lib/R/site-library 3.0 NA NA grid, stats, graphics NA NA NA GPL-2 NA NA NA NA no 4.0.0
rms rms /usr/lib/R/site-library 6.0-1 NA R (>= 3.5.0), Hmisc (>= 4.3-0), survival (>= 3.1-12), lattice, ggplot2 (>= 2.2), SparseM methods, quantreg, rpart, nlme (>= 3.1-123), polspline, multcomp, htmlTable (>= 1.11.0), htmltools, MASS, cluster, digest NA boot, tcltk, plotly (>= 4.5.6), knitr, mice, rmsb NA GPL (>= 2) NA NA NA NA yes 4.0.2
rngtools rngtools /usr/lib/R/site-library 1.5 NA R (>= 3.2.0), methods digest, utils, stats, parallel NA covr, RUnit, testthat NA GPL-3 NA NA NA NA no 4.0.0
robustbase robustbase /usr/lib/R/site-library 0.93-6 NA R (>= 3.1.0) stats, graphics, utils, methods, DEoptimR NA grid, MASS, lattice, boot, cluster, Matrix, robust, fit.models, MPV, xtable, ggplot2, GGally, RColorBrewer, reshape2, sfsmisc, catdata, doParallel, foreach, skewt NA GPL (>= 2) NA NA NA NA yes 4.0.0
roxygen2 roxygen2 /usr/lib/R/site-library 7.1.1 NA R (>= 3.2) brew, commonmark, desc (>= 1.2.0), digest, knitr, methods, pkgload (>= 1.0.2), purrr (>= 0.3.3), R6 (>= 2.1.2), Rcpp (>= 0.11.0), rlang, stringi, stringr (>= 1.0.0), utils, xml2 Rcpp covr, devtools, rmarkdown, testthat (>= 2.1.0), R.methodsS3, R.oo NA GPL (>= 2) NA NA NA NA yes 4.0.0
roxygen2md roxygen2md /usr/lib/R/site-library 1.0.0 NA NA desc, devtools, enc, rex, rlang, tibble, usethis, withr NA rstudioapi, testthat NA GPL-3 NA NA NA NA no 4.0.0
rpart rpart /usr/lib/R/site-library 4.1-15 recommended R (>= 2.15.0), graphics, stats, grDevices NA NA survival NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
rpart.plot rpart.plot /usr/lib/R/site-library 3.0.8 NA R (>= 3.4.0), rpart (>= 4.1-10) NA NA earth (>= 5.1.0) NA GPL-3 NA NA NA NA no 4.0.0
rpartScore rpartScore /usr/lib/R/site-library 1.0-1 NA R (>= 2.14.2), rpart NA NA MASS NA GPL (>= 2) NA NA NA NA NA 4.0.0
rprojroot rprojroot /usr/lib/R/site-library 1.3-2 NA R (>= 3.0.0) backports NA testthat, mockr, knitr, withr, rmarkdown NA GPL-3 NA NA NA NA no 4.0.0
rsnps rsnps /usr/lib/R/site-library 0.3.0 NA NA plyr, stringr, crul (>= 0.5.2), data.table, XML, xml2, jsonlite NA testthat, knitr NA MIT + file LICENSE NA NA NA NA no 4.0.0
rsq rsq /usr/lib/R/site-library 2.0 NA NA methods, stats, MASS, lme4, nlme, numDeriv, Matrix NA NA GPL-2 NA NA NA NA no 4.0.0
rstatix rstatix /usr/lib/R/site-library 0.6.0 NA R (>= 3.3.0) stats, utils, tidyr (>= 1.0.0), purrr, broom (>= 0.5.6), rlang (>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr, corrplot, tidyselect (>= 1.0.0), car, generics (>= 0.0.2) NA knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot, testthat, spelling NA GPL-2 NA NA NA NA no 4.0.0
rstudioapi rstudioapi /usr/lib/R/site-library 0.11 NA NA NA NA testthat, knitr, rmarkdown, clipr NA MIT + file LICENSE NA NA NA NA no 4.0.0
rsvd rsvd /usr/lib/R/site-library 1.0.3 NA R (>= 3.2.2) Matrix NA ggplot2, testthat NA GPL (>= 3) NA NA NA NA no 4.0.0
rticles rticles /usr/lib/R/site-library 0.14 NA NA utils, rmarkdown, knitr, yaml, tinytex (>= 0.19), xfun NA testit, bookdown, xtable NA GPL-3 NA NA NA NA no 4.0.0
rtracklayer rtracklayer /usr/lib/R/site-library 1.48.0 NA R (>= 3.3), methods, GenomicRanges (>= 1.37.2) XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools S4Vectors, IRanges, XVector BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit NA Artistic-2.0 + file LICENSE NA NA NA NA yes 4.0.0
rvcheck rvcheck /usr/lib/R/site-library 0.1.8 NA R (>= 3.4.0) BiocManager, utils, rlang NA NA NA Artistic-2.0 NA NA NA NA no 4.0.0
rversions rversions /usr/lib/R/site-library 2.0.2 NA NA curl, utils, xml2 (>= 1.0.0) NA mockery, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
rvest rvest /usr/lib/R/site-library 0.3.5 NA R (>= 3.2), xml2 httr (>= 0.5), magrittr, selectr NA covr, knitr, png, rmarkdown, spelling, stringi (>= 0.3.1), testthat NA GPL-3 NA NA NA NA no 4.0.0
sandwich sandwich /usr/lib/R/site-library 2.5-1 NA R (>= 2.10.0) stats, utils, zoo NA AER, car, geepack, lattice, lmtest, MASS, multiwayvcov, parallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange, survival NA GPL-2 | GPL-3 NA NA NA NA no 4.0.0
scales scales /usr/lib/R/site-library 1.1.1 NA R (>= 3.2) farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6, RColorBrewer, viridisLite NA bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA no 4.0.0
scatterpie scatterpie /usr/lib/R/site-library 0.1.4 NA R (>= 3.4.0), ggplot2 ggforce, rlang, rvcheck (>= 0.1.0), stats, tidyr, utils NA knitr, prettydoc, maps NA Artistic-2.0 NA NA NA NA no 4.0.0
scatterplot3d scatterplot3d /usr/lib/R/site-library 0.3-41 NA R (>= 2.7.0) grDevices, graphics, stats NA NA NA GPL-2 NA NA NA NA no 4.0.0
segmented segmented /usr/lib/R/site-library 1.2-0 NA NA NA NA NA NA GPL NA NA NA NA no 4.0.0
selectr selectr /usr/lib/R/site-library 0.4-2 NA R (>= 3.0) methods, stringr, R6 NA testthat, XML, xml2 NA BSD_3_clause + file LICENCE NA NA NA NA no 4.0.0
seqinr seqinr /usr/lib/R/site-library 3.6-1 NA R (>= 2.10.0) ade4,segmented NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
seriation seriation /usr/lib/R/site-library 1.2-8 NA R (>= 2.14.0) TSP, qap, grid, cluster, gclus, dendextend, colorspace, MASS, gplots, registry, methods, stats, grDevices NA biclust, testthat, DendSer, GA NA GPL-3 NA NA NA NA yes 4.0.0
servr servr /usr/lib/R/site-library 0.17 NA R (>= 3.0.0) mime (>= 0.2), httpuv (>= 1.4.0), xfun, jsonlite NA tools, later, rstudioapi, knitr (>= 1.9), rmarkdown NA GPL NA NA NA NA no 4.0.0
sessioninfo sessioninfo /usr/lib/R/site-library 1.1.1 NA NA cli, tools, utils, withr NA callr, covr, mockery, testthat NA GPL-2 NA NA NA NA no 4.0.0
sf sf /usr/lib/R/site-library 0.9-3 NA methods, R (>= 3.3.0) classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid, magrittr, Rcpp (>= 0.12.18), stats, tools, units (>= 0.6-0), utils Rcpp blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.2-1), maps, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, spatstat.utils, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs NA GPL-2 | MIT + file LICENSE NA NA NA NA yes 4.0.0
shape shape /usr/lib/R/site-library 1.4.4 NA R (>= 2.01) stats, graphics, grDevices NA NA NA GPL (>= 3) NA NA NA NA no 4.0.0
shiny shiny /usr/lib/R/site-library 1.5.0 NA R (>= 3.0.2), methods utils, grDevices, httpuv (>= 1.5.2), mime (>= 0.3), jsonlite (>= 0.9.16), xtable, digest, htmltools (>= 0.4.0.9003), R6 (>= 2.0), sourcetools, later (>= 1.0.0), promises (>= 1.1.0), tools, crayon, rlang (>= 0.4.0), fastmap (>= 1.0.0), withr, commonmark (>= 1.7), glue (>= 1.3.2) NA datasets, Cairo (>= 1.5-5), testthat (>= 2.1.1), knitr (>= 1.6), markdown, rmarkdown, ggplot2, reactlog (>= 1.0.0), magrittr, shinytest, yaml, future, dygraphs, ragg, showtext NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
shinythemes shinythemes /usr/lib/R/site-library 1.1.2 NA R (>= 3.0.0) shiny (>= 0.11) NA NA NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
slam slam /usr/lib/R/site-library 0.1-47 NA R (>= 3.4.0) stats NA NA Matrix, SparseM, spam GPL-2 NA NA NA NA yes 4.0.0
snakecase snakecase /usr/lib/R/site-library 0.11.0 NA R (>= 3.2) stringr, stringi NA testthat, covr, tibble, purrrlyr, knitr, rmarkdown, magrittr NA GPL-3 NA NA NA NA no 4.0.0
snow snow /usr/lib/R/site-library 0.4-3 NA R (>= 2.13.1), utils NA NA Rmpi,rlecuyer,nws NA GPL NA NA NA NA no 4.0.0
sourcetools sourcetools /usr/lib/R/site-library 0.1.7 NA R (>= 3.0.2) NA NA testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
sp sp /usr/lib/R/site-library 1.4-2 NA R (>= 3.0.0), methods utils, stats, graphics, grDevices, lattice, grid NA RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir NA GPL (>= 2) NA NA NA NA yes 4.0.0
spFSR spFSR /usr/lib/R/site-library 1.0.0 NA mlr (>= 2.11), parallelMap (>= 1.3), parallel (>= 3.4.2), tictoc (>= 1.0) ggplot2 (>= 2.2.1), class (>= 7.3), mlbench (>= 2.1) NA caret (>= 6.0), MASS (>= 7.3), knitr, rmarkdown NA GPL-3 NA NA NA NA no 4.0.0
spam spam /usr/lib/R/site-library 2.5-1 NA R (>= 3.1), dotCall64, grid, methods NA NA spam64, fields, SparseM, Matrix, testthat, R.rsp, truncdist, knitr, rmarkdown NA LGPL-2 | BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
spatial spatial /usr/lib/R/site-library 7.3-12 recommended R (>= 3.0.0), graphics, stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
spelling spelling /usr/lib/R/site-library 2.1 NA NA commonmark, xml2, hunspell (>= 3.0), knitr NA pdftools NA MIT + file LICENSE NA NA NA NA no 4.0.0
spls spls /usr/lib/R/site-library 2.2-3 NA R (>= 2.14) MASS, nnet, parallel, pls NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
sqldf sqldf /usr/lib/R/site-library 0.4-11 NA R (>= 3.1.0), gsubfn (>= 0.6), proto, RSQLite DBI, chron NA RH2, RMySQL, RPostgreSQL, svUnit, tcltk, MASS NA GPL-2 NA NA NA NA no 4.0.0
stabledist stabledist /usr/lib/R/site-library 0.7-1 NA R (>= 3.1.0) stats NA Matrix, fBasics, FMStable, RUnit, Rmpfr, sfsmisc NA GPL (>= 2) NA NA NA NA no 4.0.0
stabs stabs /usr/lib/R/site-library 0.6-3 NA R (>= 2.14.0), methods, stats, parallel graphics, grDevices, utils NA glmnet, lars, mboost (> 2.3-0), gamboostLSS (>= 1.2-0), QUIC, TH.data, hdi, testthat, knitr, rmarkdown, igraph, huge NA GPL-2 NA NA NA NA no 4.0.0
stargazer stargazer /usr/lib/R/site-library 5.2.2 NA NA stats, utils NA NA AER, betareg, brglm, censReg, dynlm, eha, erer, ergm, fGarch, gee, glmx, gmm, lfe, lme4, lmtest, MASS, mclogit, mgcv, mlogit, mnlogit, nlme, nnet, ordinal, plm, pscl, quantreg, rms, relevent, robustbase, sampleSelection, spdep, survey, survival, Zelig GPL (>= 2) NA NA NA NA no 4.0.0
statmod statmod /usr/lib/R/site-library 1.4.34 NA R (>= 3.0.0) stats, graphics NA MASS, tweedie NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
stepPlr stepPlr /usr/lib/R/site-library 0.93 NA R (>= 2.0) NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
stringdist stringdist /usr/lib/R/site-library 0.9.6 NA R (>= 2.15.3) parallel NA tinytest NA GPL-3 NA NA NA NA yes 4.0.2
stringi stringi /usr/lib/R/site-library 1.4.6 NA R (>= 2.14) tools, utils, stats NA NA NA file LICENSE yes NA NA NA yes 4.0.0
stringr stringr /usr/lib/R/site-library 1.4.0 NA R (>= 3.1) glue (>= 1.2.0), magrittr, stringi (>= 1.1.7) NA covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat NA GPL-2 | file LICENSE NA NA NA NA no 4.0.0
strucchange strucchange /usr/lib/R/site-library 1.5-2 NA R (>= 2.10.0), zoo, sandwich graphics, stats, utils NA stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
styler styler /usr/lib/R/site-library 1.3.2 NA NA backports (>= 1.1.0), cli (>= 1.1.0), magrittr (>= 1.0.1), purrr (>= 0.2.3), R.cache (>= 0.14.0), rematch2 (>= 2.0.1), rlang (>= 0.1.1), rprojroot (>= 1.1), tibble (>= 1.4.2), tools, withr (>= 1.0.0), xfun (>= 0.1) NA data.tree (>= 0.1.6), digest, dplyr, here, knitr, prettycode, rmarkdown, rstudioapi (>= 0.7), testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 4.0.0
subselect subselect /usr/lib/R/site-library 0.15.2 NA R (>= 3.5.0) MASS, ISwR, corpcor NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
superpc superpc /usr/lib/R/site-library 1.09 NA survival NA NA NA NA GPL-2 NA NA NA NA NA 4.0.0
survAUC survAUC /usr/lib/R/site-library 1.0-5 NA R (>= 2.6.0), survival NA NA rms NA GPL-2 NA NA NA NA NA 4.0.0
survMisc survMisc /usr/lib/R/site-library 0.5.5 NA survival graphics, grDevices, stats, utils, knitr, KMsurv, ggplot2, data.table, zoo, grid, gridExtra, km.ci, xtable NA NA NA GPL-2 NA NA NA NA no 4.0.0
survival survival /usr/lib/R/site-library 3.2-3 recommended R (>= 3.4.0) graphics, Matrix, methods, splines, stats, utils NA NA NA LGPL (>= 2) NA NA NA NA yes 4.0.0
survivalROC survivalROC /usr/lib/R/site-library 1.0.3 NA R (>= 1.6.1) NA NA NA NA GPL (>= 2) NA NA NA NA NA 4.0.0
survminer survminer /usr/lib/R/site-library 0.4.7 NA ggplot2, ggpubr(>= 0.1.6) grid, gridExtra (>= 2.0), magrittr, maxstat, methods, scales, survival, stats, broom, dplyr, tidyr, survMisc, purrr, tibble, rlang NA knitr, flexsurv, cmprsk NA GPL-2 NA NA NA NA no 4.0.0
sva sva /usr/lib/R/site-library 3.36.0 NA R (>= 3.2), mgcv, genefilter, BiocParallel matrixStats, stats, graphics, utils, limma, edgeR NA pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat NA Artistic-2.0 NA NA NA NA yes 4.0.0
svglite svglite /usr/lib/R/site-library 1.2.3.2 NA R (>= 3.0.0) Rcpp, gdtools (>= 0.1.6) Rcpp, gdtools, BH htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>= 0.2.0), knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 4.0.2
swirl swirl /usr/lib/R/site-library 2.4.5 NA R (>= 3.1.0) stringr, testthat (>= 1.0.2), httr (>= 1.1.0), yaml, RCurl, digest, tools, methods NA stringi NA MIT + file LICENSE NA NA NA NA no 4.0.0
sys sys /usr/lib/R/site-library 3.3 NA NA NA NA unix (>= 1.4), spelling, testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
systemfonts systemfonts /usr/lib/R/site-library 0.2.3 NA NA NA NA testthat (>= 2.1.0), covr, knitr, rmarkdown, tools NA MIT + file LICENSE NA NA NA NA yes 4.0.0
tensorflow tensorflow /usr/lib/R/site-library 2.2.0 NA R (>= 3.1) config, jsonlite (>= 1.2), processx, reticulate (>= 1.10), tfruns (>= 1.0), utils, yaml, rstudioapi (>= 0.7) NA testthat (>= 2.1.0), keras, tfestimators, callr NA Apache License 2.0 NA NA NA NA no 4.0.0
testextra testextra /usr/lib/R/site-library 0.1.0.1 NA NA assertthat, methods, parsetools, pkgcond, postlogic, purrr, rlang, stringi, testthat, utils NA covr, devtools, withr, rstudioapi, htmltools, shiny, yaml, DT NA GPL-2 NA NA NA NA no 4.0.0
testthat testthat /usr/lib/R/site-library 2.3.2 NA R (>= 3.1) cli, crayon (>= 1.3.4), digest, ellipsis, evaluate, magrittr, methods, pkgload, praise, R6 (>= 2.2.0), rlang (>= 0.4.1), withr (>= 2.0.0) NA covr, curl (>= 0.9.5), devtools, knitr, rmarkdown, usethis, vctrs (>= 0.1.0), xml2 NA MIT + file LICENSE NA NA NA NA yes 4.0.0
tfruns tfruns /usr/lib/R/site-library 1.4 NA R (>= 3.1) utils, jsonlite (>= 1.2), base64enc, yaml, config, magrittr, whisker, tidyselect, rlang, rstudioapi (>= 0.7), reticulate NA testthat, knitr NA Apache License 2.0 NA NA NA NA no 4.0.0
tibble tibble /usr/lib/R/site-library 3.0.3 NA R (>= 3.1.0) cli, crayon (>= 1.3.4), ellipsis (>= 0.2.0), fansi (>= 0.4.0), lifecycle (>= 0.2.0), magrittr, methods, pillar (>= 1.4.3), pkgconfig, rlang (>= 0.4.3), utils, vctrs (>= 0.2.4) NA bench, bit64, blob, covr, dplyr, evaluate, formattable, hms, htmltools, import, knitr, lubridate, mockr, nycflights13, purrr, rmarkdown, testthat (>= 2.1.0), tidyr, withr NA MIT + file LICENSE NA NA NA NA yes 4.0.2
tictoc tictoc /usr/lib/R/site-library 1.0 NA R (>= 3.0.3), methods NA NA NA NA Apache License (== 2.0) | file LICENSE NA NA NA NA no 4.0.0
tidygraph tidygraph /usr/lib/R/site-library 1.2.0 NA NA tibble, dplyr (>= 0.8.5), igraph, magrittr, utils, rlang, R6, Rcpp, tools, stats, tidyr, pillar Rcpp network, data.tree, ape, graph, methods, testthat, covr, seriation, netrankr, influenceR, NetSwan NA MIT + file LICENSE NA NA NA NA yes 4.0.0
tidyr tidyr /usr/lib/R/site-library 1.1.0 NA R (>= 3.1) dplyr (>= 0.8.2), ellipsis (>= 0.1.0), glue, magrittr, purrr, Rcpp, rlang, stringi, tibble (>= 2.1.1), tidyselect (>= 1.1.0), utils, vctrs (>= 0.3.0), lifecycle Rcpp covr, jsonlite, knitr, repurrrsive (>= 1.0.0), rmarkdown, readr, testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA yes 4.0.0
tidyselect tidyselect /usr/lib/R/site-library 1.1.0 NA R (>= 3.2) ellipsis, glue (>= 1.3.0), purrr (>= 0.3.2), rlang (>= 0.4.6), vctrs (>= 0.2.2) NA covr, crayon, dplyr, knitr, magrittr, rmarkdown, testthat (>= 2.3.0), tibble (>= 2.1.3), withr NA GPL-3 NA NA NA NA yes 4.0.0
tidyverse tidyverse /usr/lib/R/site-library 1.3.0 NA R (>= 3.2) broom (>= 0.5.2), cli (>= 1.1.0), crayon (>= 1.3.4), dbplyr (>= 1.4.2), dplyr (>= 0.8.3), forcats (>= 0.4.0), ggplot2 (>= 3.2.1), haven (>= 2.2.0), hms (>= 0.5.2), httr (>= 1.4.1), jsonlite (>= 1.6), lubridate (>= 1.7.4), magrittr (>= 1.5), modelr (>= 0.1.5), pillar (>= 1.4.2), purrr (>= 0.3.3), readr (>= 1.3.1), readxl (>= 1.3.1), reprex (>= 0.3.0), rlang (>= 0.4.1), rstudioapi (>= 0.10), rvest (>= 0.3.5), stringr (>= 1.4.0), tibble (>= 2.1.3), tidyr (>= 1.0.0), xml2 (>= 1.2.2) NA covr, feather, glue, knitr, rmarkdown, testthat NA GPL-3 | file LICENSE NA NA NA NA no 4.0.0
tiff tiff /usr/lib/R/site-library 0.1-5 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
timeDate timeDate /usr/lib/R/site-library 3043.102 NA R (>= 2.15.1), graphics, utils, stats, methods NA NA date, RUnit NA GPL (>= 2) NA NA NA NA no 4.0.0
timeSeries timeSeries /usr/lib/R/site-library 3062.100 NA R (>= 2.10), graphics, grDevices, stats, methods, utils, timeDate (>= 2150.95) NA NA RUnit, robustbase, xts, PerformanceAnalytics, fTrading NA GPL (>= 2) NA NA NA NA no 4.0.0
timereg timereg /usr/lib/R/site-library 1.9.6 NA R (>= 2.15), survival lava, numDeriv, stats, graphics, grDevices, utils, methods NA mets, NA GPL (>= 2) NA NA NA NA yes 4.0.2
tinytex tinytex /usr/lib/R/site-library 0.24 NA NA xfun (>= 0.5) NA testit, rstudioapi NA MIT + file LICENSE NA NA NA NA no 4.0.0
tm tm /usr/lib/R/site-library 0.7-7 NA R (>= 3.2.0), NLP (>= 0.2-0) Rcpp, parallel, slam (>= 0.1-37), stats, tools, utils, graphics, xml2 BH, Rcpp antiword, filehash, methods, pdftools, Rcampdf, Rgraphviz, Rpoppler, SnowballC, testthat, tm.lexicon.GeneralInquirer NA GPL-3 NA NA NA NA yes 4.0.0
tmvnsim tmvnsim /usr/lib/R/site-library 1.0-2 NA NA NA NA NA NA GPL-2 NA NA NA NA yes 4.0.0
triebeard triebeard /usr/lib/R/site-library 0.3.0 NA NA Rcpp Rcpp knitr, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA yes 4.0.0
truncnorm truncnorm /usr/lib/R/site-library 1.0-8 NA R (>= 3.4.0) NA NA testthat NA GPL (>= 2) NA NA NA NA yes 4.0.0
tweenr tweenr /usr/lib/R/site-library 1.0.1 NA R (>= 3.2.0) Rcpp (>= 0.12.3), grDevices, farver, magrittr, rlang Rcpp testthat, covr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
ucminf ucminf /usr/lib/R/site-library 1.1-4 NA NA NA NA numDeriv NA GPL (>= 2) NA NA NA NA yes 4.0.0
units units /usr/lib/R/site-library 0.6-7 NA R (>= 3.0.2) Rcpp Rcpp (>= 0.12.10) udunits2, NISTunits, measurements, xml2, magrittr, pillar (>= 1.3.0), dplyr (>= 1.0.0), vctrs (>= 0.3.1), knitr, testthat, ggforce, rmarkdown NA GPL-2 NA NA NA NA yes 4.0.0
urltools urltools /usr/lib/R/site-library 1.7.3 NA R (>= 2.10) Rcpp, methods, triebeard Rcpp testthat, knitr NA MIT + file LICENSE NA NA NA NA yes 4.0.0
usdata usdata /usr/lib/R/site-library 0.1.0 NA R (>= 2.10) tibble NA dplyr, ggplot2, maps, testthat NA GPL-3 NA NA NA NA no 4.0.0
usethis usethis /usr/lib/R/site-library 1.6.1 NA R (>= 3.2) clipr (>= 0.3.0), cli, crayon, curl (>= 2.7), desc, fs (>= 1.3.0), gh (>= 1.1.0), git2r (>= 0.23), glue (>= 1.3.0), purrr, rematch2, rlang (>= 0.4.3), rprojroot (>= 1.2), rstudioapi, stats, utils, whisker, withr, yaml NA covr, knitr, magick, pkgdown (>= 1.4.0), rmarkdown, roxygen2, spelling (>= 1.2), styler (>= 1.2.0), testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 4.0.0
utf8 utf8 /usr/lib/R/site-library 1.1.4 NA R (>= 2.10) NA NA knitr, rmarkdown, testthat NA Apache License (== 2.0) | file LICENSE NA NA NA NA yes 4.0.0
uuid uuid /usr/lib/R/site-library 0.1-4 NA R (>= 2.9.0) NA NA NA NA MIT + file LICENSE NA NA NA NA yes 4.0.0
varSelRF varSelRF /usr/lib/R/site-library 0.7-8 NA R (>= 2.0.0), randomForest, parallel NA NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
vcd vcd /usr/lib/R/site-library 1.4-7 NA R (>= 2.4.0), grid stats, utils, MASS, grDevices, colorspace, lmtest NA KernSmooth, mvtnorm, kernlab, HSAUR, coin NA GPL-2 NA NA NA NA no 4.0.0
vctrs vctrs /usr/lib/R/site-library 0.3.2 NA R (>= 3.2) ellipsis (>= 0.2.0), digest, glue, rlang (>= 0.4.7) NA bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr, pillar (>= 1.4.4), pkgdown, rmarkdown, testthat (>= 2.3.0), tibble, withr, xml2, zeallot NA GPL-3 NA NA NA NA yes 4.0.2
vdiffr vdiffr /usr/lib/R/site-library 0.3.2.2 NA R (>= 3.2.0) devtools, diffobj, fontquiver (>= 0.2.0), freetypeharfbuzz (>= 0.2.5), gdtools, glue, grDevices, htmlwidgets (>= 0.6), htmltools, purrr (>= 0.2.0), rlang, R6, Rcpp, shiny, testthat (>= 1.0.0), usethis (>= 1.4.0), xml2 (>= 1.0.0) freetypeharfbuzz, gdtools, Rcpp, BH crayon, ggplot2 (>= 3.2.0), roxygen2, rstudioapi, withr, yaml NA GPL-3 | file LICENSE NA NA NA NA yes 4.0.2
vegan vegan /usr/lib/R/site-library 2.5-6 NA permute (>= 0.9-0), lattice, R (>= 3.4.0) MASS, cluster, mgcv NA parallel, tcltk, knitr NA GPL-2 NA NA NA NA yes 4.0.0
verification verification /usr/lib/R/site-library 1.42 NA R (>= 2.10), methods, fields, boot, CircStats, MASS, dtw graphics, stats NA NA NA GPL (>= 2) NA NA NA NA no 4.0.0
vipor vipor /usr/lib/R/site-library 0.4.5 NA R (>= 3.0.0) stats, graphics NA testthat, beeswarm, lattice, ggplot2, beanplot, vioplot, ggbeeswarm, NA GPL (>= 2) NA NA NA NA no 4.0.0
viridis viridis /usr/lib/R/site-library 0.5.1 NA R (>= 2.10), viridisLite (>= 0.3.0) stats, ggplot2 (>= 1.0.1), gridExtra NA hexbin (>= 1.27.0), scales, MASS, knitr, dichromat, colorspace, rasterVis, httr, mapproj, vdiffr, svglite (>= 1.2.0), testthat, covr, rmarkdown, rgdal NA MIT + file LICENSE NA NA NA NA no 4.0.0
viridisLite viridisLite /usr/lib/R/site-library 0.3.0 NA R (>= 2.10) NA NA hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr NA MIT + file LICENSE NA NA NA NA no 4.0.0
visNetwork visNetwork /usr/lib/R/site-library 2.0.9 NA R (>= 3.0) htmlwidgets, htmltools, jsonlite, magrittr, utils, methods, grDevices, stats NA knitr, rmarkdown, webshot, igraph, rpart, shiny, shinyWidgets, colourpicker, sparkline, ggraph, tidygraph, flashClust NA MIT + file LICENSE NA NA NA NA no 4.0.0
visdat visdat /usr/lib/R/site-library 0.5.3 NA R (>= 3.2.2) ggplot2, tidyr, dplyr, purrr, readr, magrittr, stats, tibble, glue NA testthat, plotly (>= 4.5.6), knitr, rmarkdown, vdiffr, gdtools, spelling NA MIT + file LICENSE NA NA NA NA no 4.0.0
webshot webshot /usr/lib/R/site-library 0.5.2 NA R (>= 3.0) magrittr, jsonlite, callr NA httpuv, knitr, rmarkdown, shiny NA GPL-2 NA NA NA NA no 4.0.0
weights weights /usr/lib/R/site-library 1.0.1 NA Hmisc, gdata, mice NA NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
whisker whisker /usr/lib/R/site-library 0.4 NA NA NA NA markdown NA GPL-3 NA NA NA NA no 4.0.0
whoami whoami /usr/lib/R/site-library 1.3.0 NA NA httr, jsonlite, utils NA covr, mockery, testthat, withr NA MIT + file LICENSE NA NA NA NA no 4.0.0
withr withr /usr/lib/R/site-library 2.2.0 NA R (>= 3.2.0) graphics, grDevices, stats NA covr, DBI, knitr, lattice, methods, rmarkdown, RSQLite, testthat (>= 2.1.0) NA GPL (>= 2) NA NA NA NA no 4.0.0
wskm wskm /usr/lib/R/site-library 1.4.40 NA R (>= 2.10), grDevices, stats, lattice, latticeExtra, fpc NA NA NA NA GPL (>= 3) NA NA NA NA yes 4.0.0
xfun xfun /usr/lib/R/site-library 0.15 NA NA stats, tools NA testit, parallel, codetools, rstudioapi, tinytex, mime, markdown, knitr, htmltools, remotes, rmarkdown NA MIT + file LICENSE NA NA NA NA yes 4.0.0
xgboost xgboost /usr/lib/R/site-library 1.1.1.1 NA R (>= 3.3.0) Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), magrittr (>= 1.5), stringi (>= 0.5.2) NA knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 0.9.0), Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), testthat, lintr, igraph (>= 1.0.1), jsonlite, float NA Apache License (== 2.0) | file LICENSE NA NA NA NA yes 4.0.0
xlsx xlsx /usr/lib/R/site-library 0.6.3 NA NA rJava, xlsxjars, grDevices, utils NA rprojroot, testthat, covr, tibble, knitr, rmarkdown, RefManageR NA GPL-3 NA NA NA NA no 4.0.0
xlsxjars xlsxjars /usr/lib/R/site-library 0.6.1 NA rJava NA NA NA NA GPL-3 NA NA NA NA no 4.0.0
xml2 xml2 /usr/lib/R/site-library 1.3.2 NA R (>= 3.1.0) methods NA covr, curl, httr, knitr, magrittr, mockery, rmarkdown, testthat (>= 2.1.0) NA GPL (>= 2) NA NA NA NA yes 4.0.0
xmlparsedata xmlparsedata /usr/lib/R/site-library 1.0.3 NA R (>= 3.0.0) NA NA covr, testthat, xml2 NA MIT + file LICENSE NA NA NA NA no 4.0.0
xopen xopen /usr/lib/R/site-library 1.0.0 NA R (>= 3.1) processx NA ps, testthat NA MIT + file LICENSE NA NA NA NA no 4.0.0
xtable xtable /usr/lib/R/site-library 1.8-4 NA R (>= 2.10.0) stats, utils NA knitr, plm, zoo, survival NA GPL (>= 2) NA NA NA NA no 4.0.0
xts xts /usr/lib/R/site-library 0.12-0 NA zoo (>= 1.7-12) methods zoo timeSeries, timeDate, tseries, chron, fts, tis, RUnit NA GPL (>= 2) NA NA NA NA yes 4.0.0
yaml yaml /usr/lib/R/site-library 2.2.1 NA NA NA NA RUnit NA BSD_3_clause + file LICENSE NA NA NA NA yes 4.0.0
zeallot zeallot /usr/lib/R/site-library 0.1.0 NA NA NA NA testthat, knitr, rmarkdown, purrr, magrittr NA MIT + file LICENSE NA NA NA NA no 4.0.0
zip zip /usr/lib/R/site-library 2.0.4 NA NA NA NA covr, processx, R6, testthat, withr NA CC0 NA NA NA NA yes 4.0.0
zlibbioc zlibbioc /usr/lib/R/site-library 1.34.0 NA NA NA NA NA NA Artistic-2.0 + file LICENSE NA NA NA NA yes 4.0.0
zoo zoo /usr/lib/R/site-library 1.8-8 NA R (>= 3.1.0), stats utils, graphics, grDevices, lattice (>= 0.20-27) NA AER, coda, chron, fts, ggplot2 (>= 3.0.0), mondate, scales, strucchange, timeDate, timeSeries, tis, tseries, xts NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
KernSmooth.1 KernSmooth /usr/lib/R/library 2.23-17 recommended R (>= 2.5.0), stats NA NA MASS NA Unlimited NA NA NA NA yes 4.0.0
MASS.1 MASS /usr/lib/R/library 7.3-51.6 recommended R (>= 3.1.0), grDevices, graphics, stats, utils methods NA lattice, nlme, nnet, survival NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
Matrix.1 Matrix /usr/lib/R/library 1.2-18 recommended R (>= 3.2.0) methods, graphics, grid, stats, utils, lattice NA expm, MASS MatrixModels, graph, SparseM, sfsmisc GPL (>= 2) | file LICENCE NA NA NA NA yes 4.0.0
base base /usr/lib/R/library 4.0.2 base NA NA NA methods NA Part of R 4.0.2 NA NA NA NA NA 4.0.2
boot.1 boot /usr/lib/R/library 1.3-25 recommended R (>= 3.0.0), graphics, stats NA NA MASS, survival NA Unlimited NA NA NA NA no 4.0.0
class.1 class /usr/lib/R/library 7.3-17 recommended R (>= 3.0.0), stats, utils MASS NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
cluster.1 cluster /usr/lib/R/library 2.1.0 recommended R (>= 3.3.0) graphics, grDevices, stats, utils NA MASS, Matrix NA GPL (>= 2) NA NA NA NA yes 4.0.0
codetools.1 codetools /usr/lib/R/library 0.2-16 recommended R (>= 2.1) NA NA NA NA GPL NA NA NA NA no 4.0.0
compiler compiler /usr/lib/R/library 4.0.2 base NA NA NA NA NA Part of R 4.0.2 NA NA NA NA NA 4.0.2
datasets datasets /usr/lib/R/library 4.0.2 base NA NA NA NA NA Part of R 4.0.2 NA NA NA NA NA 4.0.2
foreign.1 foreign /usr/lib/R/library 0.8-80 recommended R (>= 4.0.0) methods, utils, stats NA NA NA GPL (>= 2) NA NA NA NA yes 4.0.0
grDevices grDevices /usr/lib/R/library 4.0.2 base NA NA NA KernSmooth NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
graphics graphics /usr/lib/R/library 4.0.2 base NA grDevices NA NA NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
grid grid /usr/lib/R/library 4.0.2 base NA grDevices, utils NA lattice NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
lattice.1 lattice /usr/lib/R/library 0.20-41 recommended R (>= 3.0.0) grid, grDevices, graphics, stats, utils NA KernSmooth, MASS, latticeExtra chron GPL (>= 2) NA NA NA NA yes 4.0.0
methods methods /usr/lib/R/library 4.0.2 base NA utils, stats NA codetools NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
mgcv.1 mgcv /usr/lib/R/library 1.8-31 recommended R (>= 2.14.0), nlme (>= 3.1-64) methods, stats, graphics, Matrix, splines, utils NA parallel, survival, MASS NA GPL (>= 2) NA NA NA NA yes 4.0.0
nlme.1 nlme /usr/lib/R/library 3.1-148 recommended R (>= 3.4.0) graphics, stats, utils, lattice NA Hmisc, MASS NA GPL (>= 2) | file LICENCE NA NA NA NA yes 4.0.0
nnet.1 nnet /usr/lib/R/library 7.3-14 recommended R (>= 3.0.0), stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
parallel parallel /usr/lib/R/library 4.0.2 base NA tools, compiler NA methods snow, nws, Rmpi Part of R 4.0.2 NA NA NA NA yes 4.0.2
rpart.1 rpart /usr/lib/R/library 4.1-15 recommended R (>= 2.15.0), graphics, stats, grDevices NA NA survival NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
spatial.1 spatial /usr/lib/R/library 7.3-12 recommended R (>= 3.0.0), graphics, stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 4.0.0
splines splines /usr/lib/R/library 4.0.2 base NA graphics, stats NA Matrix, methods NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
stats stats /usr/lib/R/library 4.0.2 base NA utils, grDevices, graphics NA MASS, Matrix, SuppDists, methods, stats4 NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
stats4 stats4 /usr/lib/R/library 4.0.2 base NA graphics, methods, stats NA NA NA Part of R 4.0.2 NA NA NA NA NA 4.0.2
survival.1 survival /usr/lib/R/library 3.1-12 recommended R (>= 3.4.0) graphics, Matrix, methods, splines, stats, utils NA NA NA LGPL (>= 2) NA NA NA NA yes 4.0.0
tcltk tcltk /usr/lib/R/library 4.0.2 base NA utils NA NA NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
tools tools /usr/lib/R/library 4.0.2 base NA NA NA codetools, methods, xml2, curl, commonmark NA Part of R 4.0.2 NA NA NA NA yes 4.0.2
utils utils /usr/lib/R/library 4.0.2 base NA NA NA methods, xml2, commonmark NA Part of R 4.0.2 NA NA NA NA yes 4.0.2

Clean the temporary and model files (as the results of this tutorial are simplified and we do not need them).

unlink("temp", recursive = TRUE)
unlink("models", recursive = TRUE)